Contacts of the helix formed by residues 315 - 336 (chain A) in PDB entry 1TYG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 5.8 0.5 - - - +
313A ALA* 2.3 23.5 + - - -
314A ASP* 1.3 72.1 + - - +
316A PRO* 1.3 64.4 - - - +
317A VAL* 3.6 6.8 + - - +
318A LYS* 3.0 39.6 + - - +
319A MET* 3.2 18.7 + - - +
336C ALA* 3.8 26.8 - - + +
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Residues in contact with PRO 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 4.4 9.0 - - + -
123A PRO* 4.0 16.6 - - + -
127A ILE* 3.9 26.0 - - + -
131A ALA* 4.2 2.9 - - + -
310A VAL* 3.2 43.6 - - + +
311A SER 3.9 12.1 - - - +
313A ALA* 4.5 0.2 - - + -
314A ASP* 3.6 9.4 - - - +
315A ASP* 1.3 89.7 - - - +
317A VAL* 1.3 65.0 + - - +
319A MET* 3.2 3.9 + - + +
320A ALA 2.8 18.2 + - - -
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.9 13.2 - - + +
130A GLU* 3.7 15.9 - - + +
131A ALA* 3.5 32.8 - - + +
134A VAL* 3.7 28.9 - - + +
315A ASP* 3.3 6.4 + - - +
316A PRO* 1.3 76.0 - - - +
318A LYS* 1.3 58.7 + - - +
320A ALA* 2.7 23.4 + - - +
321A ARG* 3.1 12.0 + - + +
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Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP* 3.0 34.7 + - + +
317A VAL* 1.3 78.7 - - - +
319A MET* 1.3 61.5 + - - +
321A ARG* 3.7 10.1 - - - +
322A ALA* 3.3 18.0 + - - +
332C LEU* 3.6 35.6 - - + +
335C GLU* 3.2 45.6 + - + +
336C ALA* 3.8 15.1 - - + +
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Residues in contact with MET 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLY 5.3 5.4 - - - +
289A SER* 6.1 0.2 - - - -
290A PRO* 4.2 12.1 - - + -
309A ALA 3.5 21.1 - - - +
310A VAL* 4.2 6.5 - - - -
313A ALA* 3.8 21.1 - - + -
315A ASP 3.2 9.4 + - - +
316A PRO* 3.4 9.2 - - + +
317A VAL 3.0 0.6 - - - -
318A LYS* 1.3 78.0 - - - +
320A ALA* 1.3 61.1 + - - +
322A ALA* 2.9 10.4 + - - +
323A MET* 2.8 38.6 + - + +
332C LEU 5.4 0.7 - - - -
333C SER* 3.7 39.0 - - - +
336C ALA 4.0 10.5 + - - +
337C GLY 4.2 7.6 - - - +
338C ARG* 4.2 9.4 - - + -
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 5.2 0.5 - - - +
117A LEU* 5.5 1.3 - - + -
131A ALA 3.4 27.1 - - - +
134A VAL* 4.1 4.0 - - + -
135A SER* 4.2 12.2 - - - -
310A VAL* 3.9 21.5 - - + -
316A PRO 2.8 11.8 + - - +
317A VAL 2.7 16.6 + - - +
319A MET* 1.3 68.2 - - - +
321A ARG* 1.3 64.9 + - - +
323A MET* 3.0 4.5 + - - +
324A LYS* 2.9 24.0 + - - +
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 3.3 25.4 - - + +
317A VAL* 3.1 4.9 + - - +
318A LYS* 3.7 13.9 - - - +
320A ALA* 1.3 77.0 - - - +
322A ALA* 1.3 62.9 + - - +
323A MET 3.1 0.3 + - - -
324A LYS* 3.1 25.5 - - - +
325A LEU* 3.0 33.1 + - + +
328C GLU* 4.3 16.4 + - - +
332C LEU* 3.4 40.7 - - + +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PRO* 3.9 11.2 - - + +
318A LYS 3.3 12.9 + - - +
319A MET* 2.9 19.1 + - - +
321A ARG* 1.3 78.9 - - - +
323A MET* 1.3 56.2 + - - +
326A ALA* 3.0 22.9 + - - +
329C ALA* 3.3 39.2 - - - +
332C LEU* 3.7 10.8 - - + -
333C SER 4.0 6.7 - - - +
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Residues in contact with MET 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 4.2 7.0 - - + -
117A LEU* 6.3 0.2 - - + -
287A ILE* 3.5 28.7 - - + -
288A GLY 4.5 1.1 - - - +
289A SER 3.8 9.9 - - - +
290A PRO* 3.6 28.0 - - + -
293A ALA* 4.0 10.5 - - + -
306A LEU* 3.7 30.5 - - + -
309A ALA* 3.7 26.2 - - + -
310A VAL* 4.4 2.2 - - + -
319A MET* 2.8 29.9 + - + +
320A ALA* 3.0 6.0 + - - +
322A ALA* 1.3 69.8 - - - +
324A LYS* 1.3 66.3 + - - +
325A LEU 3.1 1.3 - - - -
326A ALA* 3.0 2.1 + - - +
327A VAL* 2.9 32.0 + - - +
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 4.4 11.0 - - - +
134A VAL* 2.9 27.0 + - - +
135A SER 3.7 17.5 - - - +
136A GLU* 3.5 39.0 + - + +
320A ALA 2.9 11.7 + - - +
321A ARG* 3.1 27.4 - - - +
323A MET* 1.3 75.1 - - - +
325A LEU* 1.3 79.3 + - + +
327A VAL* 4.1 4.0 - - - +
328A GLU* 3.5 30.1 + - - +
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Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ARG* 3.0 19.8 + - + +
324A LYS* 1.3 97.4 - - + +
326A ALA* 1.3 56.6 + - - +
327A VAL 3.1 2.0 - - - -
328A GLU* 3.3 12.8 + - - +
329A ALA* 2.7 38.1 + - - +
325C LEU* 4.1 24.2 - - + +
328C GLU* 3.8 37.9 - - + +
329C ALA* 3.8 19.5 - - + +
332C LEU* 4.3 12.8 - - + -
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A PRO* 3.4 50.0 - - + +
293A ALA* 4.2 3.4 - - + -
294A ALA* 3.5 16.7 - - + +
322A ALA 3.0 9.1 + - - +
323A MET* 3.0 6.5 + - - +
325A LEU* 1.3 74.7 - - - +
327A VAL* 1.3 57.8 + - - +
329A ALA* 3.2 7.3 + - - +
330A GLY 2.9 24.8 + - - -
294C ALA* 6.1 1.1 - - + -
326C ALA* 5.7 0.7 - - - +
329C ALA* 3.8 6.0 - - + +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 3.8 38.4 - - + +
115A LEU* 3.8 25.6 - - + +
293A ALA* 4.2 17.5 - - + -
294A ALA 5.0 0.7 - - - +
297A MET* 3.6 22.3 - - + +
304A VAL* 4.5 10.8 - - + +
323A MET 2.9 19.3 + - - +
324A LYS 4.1 3.8 - - - +
326A ALA* 1.3 73.7 - - - +
328A GLU* 1.3 59.4 + - - +
330A GLY 3.2 1.6 + - - -
331A ARG* 2.9 29.7 + - + +
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Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 5.2 3.1 - - - +
324A LYS* 3.5 25.2 + - - +
325A LEU* 3.3 14.6 + - - +
327A VAL* 1.3 78.1 - - - +
329A ALA* 1.3 63.3 + - - +
331A ARG* 3.3 5.4 + - - +
332A LEU* 3.0 34.6 + - + +
321C ARG* 5.9 4.1 + - - +
325C LEU* 3.7 24.3 - - + +
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ALA* 5.2 0.2 - - + -
325A LEU 2.7 21.3 + - - +
326A ALA* 3.3 9.2 - - - +
328A GLU* 1.3 74.2 - - - +
330A GLY* 1.3 62.9 + - - +
333A SER 3.2 16.6 + - - -
290C PRO* 3.3 27.4 - - + +
322C ALA* 3.3 30.2 - - - +
325C LEU* 4.0 3.8 - - + +
326C ALA* 3.9 11.7 - - - +
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Residues in contact with GLY 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ALA* 3.7 15.7 - - - +
297A MET* 3.6 20.6 - - - -
298A GLU* 4.2 4.9 - - - -
326A ALA 2.9 12.3 + - - -
327A VAL 3.2 0.4 + - - -
329A ALA* 1.3 75.4 - - - +
331A ARG* 1.3 63.9 + - - +
332A LEU 3.1 1.2 + - - -
333A SER* 3.1 10.8 + - - -
334A TYR* 3.1 21.5 + - - +
290C PRO* 4.7 2.0 - - - -
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Residues in contact with ARG 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ARG* 2.7 50.0 - - - +
297A MET* 3.6 18.1 + - + +
300A GLY 5.1 1.8 + - - -
301A ALA 4.2 13.1 + - - -
302A ASP* 4.8 9.3 + - - +
327A VAL* 2.9 18.1 + - + +
328A GLU* 3.9 5.6 - - - +
330A GLY* 1.3 74.6 - - - +
332A LEU* 1.3 62.7 + - + +
334A TYR* 3.2 34.9 + - - +
335A GLU* 3.0 49.4 + - - +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLU* 3.0 22.4 + - + +
331A ARG* 1.3 76.1 - - + +
333A SER* 1.3 56.6 + - - +
334A TYR 2.9 9.3 + - - -
335A GLU* 3.2 15.4 + - - +
336A ALA* 2.9 24.8 + - - +
318C LYS* 3.3 35.9 - - + +
321C ARG* 3.3 60.6 - - + +
322C ALA* 3.6 19.5 - - + +
325C LEU* 4.7 7.2 - - + -
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Residues in contact with SER 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLU* 3.9 15.1 + - - +
329A ALA 3.2 4.9 + - - -
330A GLY* 3.1 11.4 + - - -
332A LEU* 1.3 75.8 - - - +
334A TYR* 1.3 56.4 + - - +
336A ALA 4.1 1.1 - - - -
337A GLY 4.8 0.9 + - - -
338A ARG* 4.4 14.2 - - - +
289C SER* 4.0 1.0 - - - -
290C PRO* 3.0 29.8 - - - +
319C MET* 3.1 48.3 - - - +
322C ALA* 3.7 2.2 - - - +
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Residues in contact with TYR 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ILE* 6.0 0.7 - - - +
297A MET 3.8 12.6 - - - +
298A GLU* 3.8 20.2 - - - +
299A LEU 4.6 1.8 - - - -
300A GLY* 3.6 24.8 + - - -
330A GLY 3.4 10.5 - - - +
331A ARG* 3.3 48.2 - - - +
332A LEU 2.9 0.4 - - - -
333A SER* 1.3 80.5 - - - +
335A GLU* 1.3 69.8 + - + +
336A ALA 3.1 1.5 + - - -
337A GLY* 3.6 9.4 + - - -
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 5.7 0.2 - - - -
331A ARG* 3.0 52.9 + - - +
332A LEU* 3.2 9.8 + - - +
334A TYR* 1.3 82.1 - - + +
336A ALA* 1.3 64.1 + - - +
337A GLY* 3.1 1.4 + - - -
315C ASP* 4.9 1.6 - - - +
318C LYS* 2.3 47.6 + - + +
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU 2.9 17.1 + - - +
334A TYR 3.1 0.6 - - - -
335A GLU* 1.3 79.7 - - - +
337A GLY* 1.3 63.0 + - - +
313C ALA 3.1 2.6 - - - +
314C ASP* 2.6 26.0 - - - +
315C ASP* 3.1 38.8 + - - +
318C LYS* 3.8 10.8 - - + -
319C MET* 3.8 20.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il