Contacts of the helix formed by residues 315 - 336 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A GLU 4.9 1.2 - - - +
336A ALA* 3.1 23.2 + - - +
313C ALA* 3.0 6.8 - - - -
314C ASP* 1.3 77.8 - - - +
316C PRO* 1.3 61.3 - - - +
317C VAL* 3.4 12.6 - - - +
318C LYS* 2.8 53.7 + - - +
319C MET* 2.8 27.5 + - - +
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Residues in contact with PRO 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C TYR* 4.3 8.5 - - + -
123C PRO* 4.1 10.5 - - + -
127C ILE* 3.7 30.7 - - + -
131C ALA* 4.2 2.0 - - + -
310C VAL* 3.0 38.7 - - + +
311C SER 3.8 13.5 - - - +
313C ALA* 3.8 2.0 - - + -
314C ASP* 3.8 8.7 - - - +
315C ASP* 1.3 89.3 - - - +
317C VAL* 1.3 59.3 + - + +
319C MET* 4.3 0.2 - - + -
320C ALA* 2.7 36.4 + - - +
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Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ILE* 4.2 24.7 - - + +
130C GLU* 3.4 40.2 - - + +
131C ALA* 4.4 6.0 - - - +
134C VAL* 3.5 20.9 - - + +
315C ASP* 3.4 10.8 - - - +
316C PRO* 1.3 83.7 - - + +
318C LYS* 1.3 64.9 + - - +
320C ALA* 3.3 18.3 - - - +
321C ARG* 3.4 4.7 + - - +
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Residues in contact with LYS 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 3.3 28.9 - - + +
335A GLU* 2.3 53.3 + - + +
336A ALA* 3.8 11.7 - - + +
315C ASP* 2.8 39.3 + - - +
317C VAL* 1.3 69.1 - - - +
319C MET* 1.3 62.2 + - - +
321C ARG* 2.8 31.9 + - - +
322C ALA* 3.0 12.6 + - - +
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Residues in contact with MET 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A SER* 3.1 42.4 - - - +
336A ALA* 3.8 4.9 - - + -
337A GLY 3.5 22.7 - - - +
338A ARG* 3.6 21.8 - - + -
288C GLY 5.0 2.2 - - - +
289C SER* 5.0 1.6 - - - -
290C PRO* 4.3 9.4 - - - -
309C ALA 3.8 21.5 - - - +
310C VAL* 4.2 8.7 - - + -
313C ALA* 3.7 10.8 - - + -
315C ASP 2.8 19.0 + - - +
316C PRO* 4.0 2.7 - - + +
318C LYS* 1.3 73.5 - - - +
320C ALA* 1.3 61.7 + - - +
322C ALA* 3.7 4.3 - - - +
323C MET* 3.1 33.4 + - + +
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 5.0 1.4 - - - +
117C LEU* 5.5 0.9 - - + -
131C ALA* 3.4 29.6 - - - +
134C VAL* 4.1 3.8 - - + -
135C SER* 4.4 8.4 - - - +
310C VAL* 3.8 18.8 - - + +
316C PRO 2.7 23.8 + - - +
317C VAL 3.3 8.3 - - - +
319C MET* 1.3 74.9 - - - +
321C ARG* 1.3 61.9 + - - +
323C MET* 3.3 3.7 + - - +
324C LYS* 3.1 21.6 + - - +
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Residues in contact with ARG 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLU* 5.9 4.9 + - - +
332A LEU* 3.3 42.1 - - + +
134C VAL* 3.6 28.5 - - + +
317C VAL 3.4 3.3 + - - +
318C LYS* 2.8 22.2 + - - +
320C ALA* 1.3 75.1 - - - +
322C ALA* 1.3 56.2 + - - +
324C LYS* 3.0 36.9 + - + +
325C LEU* 3.0 21.4 + - + +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A ALA* 3.3 33.5 - - - +
332A LEU* 3.6 23.2 - - + +
333A SER* 3.7 16.8 - - - +
290C PRO* 4.0 3.1 - - + -
318C LYS 3.0 7.0 + - - +
319C MET* 3.7 8.7 - - - +
321C ARG* 1.3 76.3 - - - +
323C MET* 1.3 55.4 + - - +
325C LEU* 3.3 3.1 + - - -
326C ALA* 3.0 27.5 + - - +
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Residues in contact with MET 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 4.6 11.7 - - + -
287C ILE* 4.0 8.5 - - + -
288C GLY 4.2 0.2 - - - +
289C SER* 3.6 26.0 - - - +
290C PRO* 3.7 18.2 - - + -
293C ALA* 3.9 17.9 - - - -
306C LEU* 3.7 24.7 - - + -
309C ALA* 3.5 31.6 - - + -
310C VAL* 4.1 5.6 - - + -
319C MET* 3.1 22.4 + - + +
320C ALA* 3.6 8.3 - - - +
322C ALA* 1.3 72.5 - - - +
324C LYS* 1.3 64.7 + - - +
326C ALA* 3.4 2.0 - - - +
327C VAL* 3.1 31.5 + - - +
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Residues in contact with LYS 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C LEU* 4.1 12.0 - - + +
134C VAL 4.3 5.7 + - - +
135C SER 3.4 24.7 - - - +
136C GLU* 3.1 35.7 + - + +
320C ALA 3.1 11.6 + - - +
321C ARG* 3.0 22.7 + - + +
323C MET* 1.3 78.8 - - - +
325C LEU* 1.3 79.6 + - + +
327C VAL* 4.6 2.4 - - - +
328C GLU* 3.9 33.0 + - - +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU* 4.1 24.4 - - + +
328A GLU* 3.7 44.0 - - + +
329A ALA* 4.0 13.7 - - + +
332A LEU* 4.7 11.0 - - + -
321C ARG* 3.0 20.3 + - + +
322C ALA 3.5 6.1 - - - +
323C MET 3.2 0.2 - - - -
324C LYS* 1.3 100.6 - - + +
326C ALA* 1.3 65.7 + - - +
328C GLU* 3.0 11.5 + - - +
329C ALA* 2.9 24.5 + - - +
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ALA* 5.7 0.2 - - - +
329A ALA* 3.9 6.7 - - - +
290C PRO* 3.3 46.7 - - + +
293C ALA* 4.0 5.8 - - + -
294C ALA* 3.3 15.0 - - + +
322C ALA 3.0 7.0 + - - +
323C MET 3.4 10.1 - - - +
325C LEU* 1.3 76.8 - - - +
327C VAL* 1.3 57.2 + - - +
329C ALA* 3.3 5.0 + - - +
330C GLY 2.9 26.5 + - - -
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Residues in contact with VAL 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ARG* 4.0 25.6 - - + +
115C LEU* 4.3 25.4 - - + +
293C ALA* 4.3 16.4 - - + -
294C ALA* 5.0 1.1 - - - +
297C MET* 3.7 37.7 - - + +
304C VAL* 4.4 11.2 - - + +
306C LEU* 5.3 0.4 - - + -
323C MET* 3.1 16.7 + - - +
324C LYS 4.6 3.1 - - - +
326C ALA* 1.3 75.3 - - - +
328C GLU* 1.3 60.0 + - - +
330C GLY 3.5 0.2 + - - -
331C ARG* 2.8 32.2 + - + +
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Residues in contact with GLU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ARG* 4.3 14.9 + - - +
325A LEU* 3.8 22.5 - - + +
324C LYS* 3.9 29.4 + - - +
325C LEU* 3.0 13.2 + - - +
327C VAL* 1.3 78.4 - - - +
329C ALA* 1.3 64.8 + - - +
331C ARG* 2.8 10.1 + - - +
332C LEU* 2.8 29.7 + - + +
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Residues in contact with ALA 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PRO* 4.2 7.9 - - + -
322A ALA* 3.3 31.0 - - - +
325A LEU* 3.8 10.5 - - + +
326A ALA* 3.8 20.4 - - - +
294C ALA* 5.1 0.7 - - + -
325C LEU 2.9 15.0 + - - +
326C ALA* 3.6 9.0 - - - +
328C GLU* 1.3 68.4 - - - +
330C GLY* 1.3 66.1 + - - +
332C LEU* 2.7 16.7 + - - +
333C SER* 3.1 13.2 + - - -
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Residues in contact with GLY 330 (chain C).
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* 4.6 0.8 - - - +
294C ALA* 3.5 28.8 - - - +
297C MET* 3.7 7.2 - - - -
298C GLU* 3.8 10.4 + - - +
326C ALA 2.9 15.1 + - - -
327C VAL 3.8 0.9 - - - -
329C ALA* 1.3 75.3 - - - +
331C ARG* 1.3 60.4 + - - +
333C SER* 2.6 23.1 + - - -
334C TYR* 3.5 6.6 + - - +
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Residues in contact with ARG 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ARG* 2.6 50.5 - - - +
297C MET* 3.6 19.2 + - + +
300C GLY 4.6 4.0 + - - -
301C ALA 3.7 22.6 + - - -
302C ASP* 3.7 16.0 + - - -
327C VAL 2.8 17.3 + - - +
328C GLU* 2.8 11.2 + - - +
330C GLY* 1.3 71.7 - - - -
332C LEU* 1.3 58.3 + - + +
334C TYR* 3.9 24.1 - - - +
335C GLU* 2.9 47.4 + - - +
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A LYS* 3.6 36.0 - - + +
321A ARG* 3.4 58.6 - - + +
322A ALA* 3.7 13.7 - - + +
325A LEU* 4.3 15.7 - - + -
328C GLU* 2.8 16.0 + - + +
329C ALA 2.7 16.1 + - - +
331C ARG* 1.3 72.1 - - + +
333C SER* 1.3 69.4 + - - +
335C GLU* 2.8 32.8 + - - +
336C ALA 3.2 4.9 + - - +
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Residues in contact with SER 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER* 5.5 0.4 - - - -
290A PRO* 3.3 23.1 - - - +
319A MET* 3.7 22.0 - - - +
322A ALA* 4.0 2.0 - - - +
298C GLU* 3.3 23.8 + - - -
329C ALA 3.1 10.1 + - - -
330C GLY 2.6 15.1 + - - -
332C LEU* 1.3 75.3 - - - +
334C TYR* 1.3 65.6 + - - +
336C ALA 2.7 21.3 + - - +
337C GLY 3.3 7.6 - - - +
338C ARG* 5.4 5.2 - - - -
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Residues in contact with TYR 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C ILE* 5.8 2.6 - - + +
297C MET 3.9 15.9 - - - +
298C GLU* 3.5 27.8 - - - +
299C LEU 4.4 3.1 - - - -
300C GLY* 3.7 24.7 - - - -
330C GLY 3.5 2.1 + - - +
331C ARG* 4.0 30.1 - - - +
333C SER* 1.3 77.9 + - - +
335C GLU* 1.3 70.5 - - - +
336C ALA* 2.9 4.7 + - - -
337C GLY 4.5 4.9 + - - +
338C ARG* 5.7 1.0 - - - +
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Residues in contact with GLU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A LYS* 3.2 39.0 + - - +
114C ARG* 4.8 0.9 + - - -
331C ARG* 2.9 50.6 + - - +
332C LEU* 2.8 34.0 + - + +
334C TYR* 1.3 80.4 - - - +
336C ALA* 1.3 67.0 + - - +
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Residues in contact with ALA 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ALA 3.9 3.0 - - - +
314A ASP* 5.1 1.8 - - - +
315A ASP* 3.8 35.4 - - + +
318A LYS* 3.8 16.7 - - + +
319A MET* 4.0 7.4 - - - +
332C LEU 3.2 5.9 + - - +
333C SER 2.7 19.2 + - - +
334C TYR 3.4 3.6 - - - -
335C GLU* 1.3 77.9 - - - +
337C GLY* 1.3 60.7 - - - +
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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