Contacts of the strand formed by residues 314 - 326 (chain A) in PDB entry 3NBN
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 TRP 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A LEU* 3.8 21.1 - - + -
176A PHE 3.5 23.6 - - - +
177A ASN* 3.7 18.4 - - + -
187A ARG 4.2 2.7 - - - -
188A TYR 4.5 0.4 - - - -
189A LEU* 3.8 37.0 - - + -
198A ALA* 5.2 0.4 - - + -
270A HIS 3.6 0.7 - - - +
271A LYS* 3.1 6.4 - - - -
272A CYS* 2.9 41.0 + - - +
274A PHE* 4.5 17.7 - + + -
284A LEU* 3.6 34.6 + - + +
286A LEU* 4.4 7.0 - - + -
291A ILE* 3.5 33.4 - - + -
311A GLY 3.8 14.9 + - - -
312A ALA 3.9 13.9 - - - -
313A SER* 1.3 72.1 - - - +
315A THR* 1.3 66.9 + - - +
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Residues in contact with THR 315 (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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175A LEU* 3.2 4.9 - - - +
176A PHE* 2.8 72.2 + - + -
178A ARG 5.6 1.0 + - - -
269A LEU* 3.9 34.8 - - + +
270A HIS 3.6 5.6 - - - +
271A LYS* 3.2 33.8 + - - +
313A SER 4.3 0.7 + - - -
314A TRP* 1.3 73.2 - - - +
316A ILE* 1.3 61.8 + - - +
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Residues in contact with ILE 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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167A ILE* 4.5 17.1 - - + +
173A VAL* 3.6 35.2 - - + -
174A ALA 4.4 0.2 - - - +
175A LEU* 3.6 31.4 - - + -
208A ILE* 5.1 5.8 - - + -
266A VAL* 4.1 24.2 - - + -
268A GLN* 4.7 0.5 - - - -
269A LEU* 3.1 24.2 + - - -
270A HIS* 3.2 19.7 + - + +
272A CYS* 4.8 13.2 - - + -
274A PHE* 5.4 2.7 - - + -
315A THR* 1.3 76.0 - - - +
317A ILE* 1.3 61.9 + - - +
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Residues in contact with ILE 317 (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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39A ALA* 3.8 10.5 - - + -
41A VAL* 3.9 31.2 - - + +
55A PRO* 3.4 32.1 - - + -
167A ILE* 5.2 0.4 - - - -
173A VAL* 3.3 5.3 - - - +
174A ALA* 2.9 43.2 + - + +
176A PHE* 4.6 6.7 - - + -
268A GLN* 3.5 29.2 - - + +
269A LEU* 4.0 25.6 - - + -
316A ILE* 1.3 78.6 - - - +
318A SER* 1.3 70.7 + - - +
319A THR* 4.6 1.1 - - - +
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 3.9 0.2 - - - -
40A LYS* 3.1 38.6 + - - +
167A ILE* 4.0 9.1 - - - +
171A THR* 2.7 31.2 + - - +
173A VAL* 3.5 11.9 - - - +
268A GLN* 2.6 32.3 + - - -
317A ILE* 1.3 79.2 - - - +
319A THR* 1.3 60.2 + - - +
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Residues in contact with THR 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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37A LEU* 5.1 2.5 - - + -
38A HIS 2.7 27.7 + - - -
39A ALA* 3.6 3.9 + - - +
40A LYS* 3.1 27.1 + - - -
55A PRO* 5.8 0.9 - - - +
172A LYS* 2.9 42.5 + - + +
173A VAL 4.6 0.2 - - - +
174A ALA* 4.5 12.2 - - - +
203A TRP* 3.8 16.8 - - + -
205A ALA* 3.8 21.5 - - + -
317A ILE* 3.8 1.6 + - - +
318A SER* 1.3 74.8 - - - +
320A ASP* 1.3 68.2 + - - +
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Residues in contact with ASP 320 (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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37A LEU* 3.6 6.3 - - - +
38A HIS* 2.9 49.4 + - + +
40A LYS* 3.7 24.4 + - + +
145A LYS* 3.4 38.3 + - - +
172A LYS* 3.9 20.6 + - - +
319A THR* 1.3 83.0 - - - +
321A LYS* 1.3 69.7 + - - +
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Residues in contact with LYS 321 (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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35A LEU* 4.4 13.2 - - + -
36A ILE 3.4 7.2 - - - +
37A LEU* 3.8 18.4 - - + -
38A HIS* 4.5 1.6 - - - -
145A LYS* 3.3 30.1 + - - +
172A LYS* 4.0 22.0 - - - +
320A ASP* 1.3 79.8 + - - +
322A ALA* 1.3 63.7 + - - +
323A GLU* 3.8 29.7 + - - +
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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
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35A LEU* 3.7 1.6 - - - +
36A ILE* 2.8 35.3 + - + +
38A HIS* 4.9 0.9 - - + -
143A LEU 3.6 23.8 - - - +
144A SER* 4.1 13.0 - - - -
145A LYS* 4.2 14.6 - - + +
321A LYS* 1.3 77.0 - - - +
323A GLU* 1.3 66.0 + - - +
324A TYR* 3.3 13.8 - - + +
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Residues in contact with GLU 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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33A THR* 4.4 7.2 + - - +
34A VAL 4.2 6.5 - - - +
35A LEU* 3.8 32.9 - - + +
145A LYS* 5.8 0.6 - - - +
321A LYS* 3.8 30.8 + - - +
322A ALA* 1.3 71.2 - - - +
324A TYR* 1.3 83.3 + - - +
325A THR* 4.7 11.3 - - + +
342A VAL* 5.1 8.1 - - - +
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Residues in contact with TYR 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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33A THR* 3.4 2.2 - - - -
34A VAL* 3.3 30.7 + - + -
36A ILE* 4.9 1.6 - - + -
142A PHE* 3.8 31.0 - + + -
143A LEU* 2.7 48.7 + - - +
322A ALA* 3.3 20.0 - - + +
323A GLU* 1.3 94.8 - - - +
325A THR* 1.3 63.9 + - - +
326A PHE* 4.0 4.2 - - - -
340A VAL* 3.4 45.3 - - + -
342A VAL* 4.6 8.7 - - + -
363A ASN* 4.5 12.3 + - - -
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Residues in contact with THR 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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31A ASP* 3.9 9.1 + - - +
32A GLN 3.8 6.5 - - - -
33A THR* 3.7 23.6 - - + +
323A GLU* 4.7 12.1 - - + +
324A TYR* 1.3 79.2 - - - +
326A PHE* 1.3 67.8 + - - +
340A VAL* 3.6 14.0 - - - +
341A PRO 5.4 0.2 - - - +
422A TYR* 3.8 10.8 - - - +
423A SER* 3.5 32.0 + - - +
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Residues in contact with PHE 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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31A ASP* 3.9 3.9 + - - -
32A GLN* 3.2 65.2 + - + +
33A THR* 4.1 7.0 - - - -
34A VAL 4.4 6.5 - - - -
66A TRP* 4.7 10.5 - + - -
131A MET* 5.8 0.4 - - + -
139A ILE* 5.3 6.7 - - + -
142A PHE* 4.4 20.6 - + - -
324A TYR 4.0 6.1 - - - -
325A THR* 1.3 83.4 + - - +
327A TYR* 1.3 60.5 + - - +
328A GLU* 5.9 2.9 - - + -
337A VAL* 3.3 47.8 - - + -
340A VAL* 5.0 5.4 - - + -
420A ILE* 4.4 3.6 - - + -
421A ILE 3.5 9.6 - - - -
422A TYR* 3.7 20.0 - + + -
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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
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Atomic class I II III IV V VI VII VIII
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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