Contacts of the helix formed by residues 308 - 330 (chain A) in PDB entry 1T2E
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 ASN 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ARG* 3.6 15.5 - - - +
307A LEU* 1.3 76.6 - - - +
309A SER* 1.3 60.0 + - - +
310A GLU* 3.1 18.8 + - - +
311A GLU* 2.6 54.1 + - - +
312A LYS* 2.8 27.1 + - - +
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ASN* 1.3 76.9 - - - +
310A GLU* 1.3 79.5 + - - +
312A LYS* 3.7 6.1 - - - +
313A ALA* 2.8 29.3 + - - +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ASN* 3.4 21.2 + - - +
309A SER* 1.3 96.0 + - - +
311A GLU* 1.3 63.2 + - + +
313A ALA* 3.2 15.2 + - - +
314A LYS* 3.2 17.7 + - - +
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 4.2 3.2 - - - +
202A LEU* 3.8 29.7 - - + +
204A ARG* 2.8 47.1 + - - +
205A TYR* 4.2 1.8 - - - -
307A LEU* 3.2 15.5 - - + +
308A ASN* 2.6 49.0 + - - +
310A GLU* 1.3 74.7 - - + +
312A LYS* 1.3 62.4 + - - +
314A LYS* 3.0 10.0 + - - +
315A PHE* 2.9 26.5 + - - +
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Residues in contact with LYS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 2.7 37.8 + - + +
280A GLY* 4.2 6.6 + - - -
281A HIS* 4.0 3.2 + - - -
307A LEU* 4.0 13.4 - - + +
308A ASN 2.8 18.0 + - - +
309A SER* 3.8 7.0 - - - +
311A GLU* 1.3 78.4 - - - +
313A ALA* 1.3 64.4 + - - +
315A PHE* 3.1 9.4 + - + +
316A ASP* 2.8 54.8 + - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A SER 2.8 14.7 + - - +
310A GLU* 3.6 11.2 - - - +
311A GLU 3.1 0.4 - - - -
312A LYS* 1.3 78.3 - - - +
314A LYS* 1.3 65.4 + - + +
316A ASP* 3.2 11.3 + - - +
317A GLU* 3.0 30.5 + - - +
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 4.6 1.5 - - - +
200A VAL* 3.3 28.2 - - + +
310A GLU 3.2 13.0 + - - +
311A GLU* 3.0 9.3 + - - +
313A ALA* 1.3 77.0 - - + +
315A PHE* 1.3 66.4 + - - +
317A GLU* 3.0 36.4 + - + +
318A ALA 3.0 18.2 + - - -
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Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL* 3.7 22.9 - - + -
193A GLY* 3.5 26.9 - - - -
200A VAL* 3.7 9.1 - - + +
275A LEU* 3.8 16.4 - - + -
279A TYR* 3.3 52.5 - + + -
281A HIS* 3.9 9.0 - + - -
287A GLY* 5.1 0.2 - - - -
288A GLY 3.7 10.5 - - - -
307A LEU* 4.1 11.2 - - + -
311A GLU 2.9 12.5 + - - +
312A LYS* 3.4 13.9 - - + +
314A LYS* 1.3 76.1 - - - +
316A ASP* 1.3 64.5 + - - +
318A ALA* 3.1 3.9 + - - +
319A ILE* 2.9 43.6 + - + +
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Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR 4.2 0.2 - - - +
281A HIS* 2.7 32.9 + - + +
312A LYS* 2.8 47.6 + - - +
313A ALA* 3.5 11.2 - - - +
315A PHE* 1.3 79.4 - - - +
317A GLU* 1.3 57.8 + - + +
319A ILE* 3.3 1.3 + - - +
320A ALA* 2.8 31.1 + - - +
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Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 2.8 39.3 + - + +
313A ALA* 3.0 21.9 + - + +
314A LYS* 3.0 41.6 + - + +
316A ASP* 1.3 79.1 - - + +
318A ALA* 1.3 62.1 + - - +
320A ALA* 3.3 8.0 + - - +
321A GLU* 3.2 24.6 + - - +
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLY* 3.9 7.4 - - - -
194A ALA* 3.8 31.2 - - + +
198A LYS* 3.6 33.1 - - + +
200A VAL* 4.1 2.7 - - + -
314A LYS 3.0 9.6 + - - +
315A PHE 3.1 7.6 + - - +
317A GLU* 1.3 78.1 - - - +
319A ILE* 1.3 64.1 + - - +
321A GLU* 3.1 13.3 + - - +
322A THR* 3.2 14.4 + - - -
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Residues in contact with ILE 319 (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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193A GLY* 3.6 22.0 - - - +
275A LEU* 3.8 8.7 - - + -
281A HIS* 3.3 33.7 - - + +
285A ILE* 4.0 18.6 - - + -
286A PHE 4.0 6.7 - - - +
287A GLY* 3.8 15.9 - - - -
315A PHE* 2.9 48.6 + - + +
316A ASP 3.9 1.1 - - - +
318A ALA* 1.3 75.7 - - - +
320A ALA* 1.3 58.3 + - - +
322A THR* 3.1 6.1 + - - +
323A LYS* 2.8 35.6 + - + +
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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
----------------------------------------------------------
316A ASP 2.8 18.1 + - - +
317A GLU* 3.5 9.2 - - - +
319A ILE* 1.3 77.8 - - - +
321A GLU* 1.3 61.9 + - - +
323A LYS* 3.7 7.6 - - - +
324A ARG* 2.8 29.8 + - - +
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASP* 4.2 5.4 - - - +
198A LYS* 3.5 42.8 + - + +
317A GLU 3.2 2.1 + - - +
318A ALA* 3.1 9.7 + - - +
320A ALA* 1.3 78.2 - - - +
322A THR* 1.3 67.6 + - - +
324A ARG* 3.1 48.1 + - - +
325A MET* 3.1 26.1 + - + +
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Residues in contact with THR 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASP* 3.7 39.2 - - + +
144A VAL* 3.7 16.7 - - + +
147A GLN* 5.7 0.2 - - - +
193A GLY 4.8 0.5 + - - -
194A ALA* 3.6 18.9 - - - +
285A ILE* 4.0 15.3 - - + -
286A PHE 3.8 13.5 + - - +
318A ALA 3.2 9.3 + - - -
319A ILE* 3.1 11.8 + - - -
321A GLU* 1.3 77.8 - - - +
323A LYS* 1.3 58.2 + - - +
325A MET* 3.2 7.1 + - - +
326A LYS* 2.8 25.2 + - + +
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Residues in contact with LYS 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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281A HIS* 4.5 15.8 + - - -
282A SER 4.5 10.4 + - - +
283A ASP 5.5 1.3 - - - -
285A ILE* 4.1 31.0 - - + -
319A ILE* 2.8 24.3 + - - +
320A ALA* 3.8 8.7 - - - +
322A THR* 1.3 71.0 - - - +
324A ARG* 1.3 65.3 + - - +
326A LYS* 2.8 17.2 + - + +
327A PRO* 2.9 13.9 - - + +
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Residues in contact with ARG 324 (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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110A ASP* 3.2 29.1 + - - +
320A ALA 2.8 18.8 + - - +
321A GLU* 3.3 29.0 + - - +
323A LYS* 1.3 76.5 - - - +
325A MET* 1.3 77.8 + - - +
327A PRO* 3.4 11.6 - - - +
328A LEU* 3.8 35.7 - - + +
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Residues in contact with MET 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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110A ASP* 3.3 45.1 - - - +
113A LEU* 3.4 26.2 - - + -
141A PRO* 4.0 16.6 - - + -
144A VAL* 3.9 21.5 - - + -
321A GLU* 3.1 26.1 + - + +
322A THR* 3.5 6.7 - - - +
324A ARG* 1.3 98.8 - - - +
326A LYS* 1.3 66.7 + - - +
327A PRO 3.3 0.2 - - - -
328A LEU* 3.0 8.2 + - + -
329A ALA* 2.9 23.2 + - - +
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Residues in contact with LYS 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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144A VAL* 4.3 9.0 - - + -
147A GLN* 3.3 31.8 - - + +
151A GLN* 3.4 27.8 + - - +
283A ASP* 4.0 9.8 + - - +
285A ILE* 4.3 10.8 - - + -
322A THR* 2.8 12.3 + - + +
323A LYS* 2.8 19.3 + - + +
325A MET* 1.3 78.2 - - - +
327A PRO* 1.3 68.2 - - + +
329A ALA* 3.2 8.1 + - - +
330A HIS* 3.0 37.8 + - + +
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Residues in contact with PRO 327 (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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323A LYS* 2.9 20.0 - - + +
324A ARG* 3.4 9.4 - - - +
326A LYS* 1.3 91.1 - - + +
328A LEU* 1.3 65.2 + - + +
329A ALA 3.4 0.3 + - - -
330A HIS* 3.5 13.6 - - + +
331A HIS* 3.4 15.2 - - - +
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Residues in contact with LEU 328 (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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113A LEU* 3.5 21.2 - - + +
324A ARG* 3.8 40.6 - - + +
325A MET* 3.0 14.5 + - + +
327A PRO* 1.3 78.3 - - + +
329A ALA* 1.3 61.0 + - - +
331A HIS* 2.8 31.3 + - + +
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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
----------------------------------------------------------
113A LEU* 3.7 12.7 - - + +
117A ASN* 3.1 23.7 - - - +
121A ILE* 5.3 2.9 - - - +
144A VAL* 3.4 33.7 - - + -
145A MET* 3.8 13.9 - - + -
148A LEU* 4.3 13.8 - - + +
325A MET 2.9 5.2 + - - +
326A LYS 3.5 5.8 - - - +
328A LEU* 1.3 72.4 - - - +
330A HIS* 1.3 58.4 + - + +
331A HIS 2.5 19.2 + - - +
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Residues in contact with HIS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 5.7 4.5 - - + -
144A VAL* 6.0 1.1 - - + -
147A GLN* 5.6 0.4 - - + -
148A LEU* 3.3 38.4 - - + +
151A GLN* 4.0 20.7 + - - +
152A HIS* 4.7 8.1 + - - -
326A LYS* 3.0 55.2 + - + +
327A PRO* 3.5 8.6 - - + +
329A ALA* 1.3 77.5 - - + +
331A HIS* 1.3 64.7 - - - +
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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