Contacts of the strand formed by residues 314 - 326 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LEU* 3.8 21.3 - - + -
176D PHE 3.6 22.9 - - - -
177D ASN* 3.7 19.1 - - + -
187D ARG 4.2 2.0 - - - -
188D TYR 5.1 0.4 - - - -
189D LEU* 3.7 37.7 - - + -
198D ALA* 5.2 0.4 - - + -
270D HIS 3.6 0.9 - - - +
271D LYS* 3.1 6.8 - - - -
272D CYS* 2.9 40.9 + - - +
274D PHE* 4.4 18.8 - + + -
284D LEU* 3.7 37.1 + - + +
286D LEU* 4.5 6.3 - - + -
291D ILE* 3.5 34.3 - - + -
311D GLY 3.9 14.5 + - - -
312D ALA 3.8 13.9 - - - -
313D SER* 1.3 73.2 - - - +
315D THR* 1.3 67.0 + - - +
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Residues in contact with THR 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LEU* 3.1 4.7 - - - +
176D PHE* 2.7 76.9 + - + -
178D ARG 5.6 1.2 + - - -
269D LEU* 3.9 34.5 - - + +
270D HIS 3.7 6.1 - - - +
271D LYS* 3.3 32.7 + - - +
313D SER 4.3 0.9 + - - -
314D TRP* 1.3 73.0 - - - +
316D ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ILE* 4.5 16.9 - - + +
173D VAL* 3.7 36.3 - - + -
174D ALA 4.4 0.2 - - - +
175D LEU* 3.7 31.9 - - + -
208D ILE* 5.2 5.6 - - + -
230D TYR* 5.8 0.2 - - - +
266D VAL* 4.1 24.0 - - + -
268D GLN* 4.7 0.5 - - - -
269D LEU* 3.1 24.6 + - - -
270D HIS 3.2 20.1 + - - +
272D CYS* 4.8 14.8 - - + -
274D PHE* 5.5 1.8 - - + -
315D THR* 1.3 75.5 - - - +
317D ILE* 1.3 61.6 + - - +
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Residues in contact with ILE 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ALA* 3.8 15.0 - - + -
41D VAL* 3.9 26.5 - - + +
55D PRO* 3.3 31.9 - - + -
167D ILE* 5.2 0.2 - - - -
173D VAL* 3.3 6.2 - - - +
174D ALA* 2.9 46.5 + - + +
176D PHE* 4.6 6.7 - - + -
268D GLN* 3.5 28.0 - - + +
269D LEU* 3.9 26.7 - - + -
316D ILE* 1.3 77.9 - - - +
318D SER* 1.3 72.2 + - - +
319D THR* 4.7 0.8 - - - +
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Residues in contact with SER 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ALA* 3.8 0.2 - - - -
40D LYS* 3.0 40.4 + - - +
167D ILE* 4.0 12.1 - - - +
171D THR* 2.7 31.4 + - - +
172D LYS 3.7 0.3 + - - -
173D VAL* 3.5 9.3 - - - +
268D GLN* 2.6 31.8 + - - -
317D ILE* 1.3 79.5 - - - +
319D THR* 1.3 61.1 + - - +
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Residues in contact with THR 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 5.0 2.9 - - + -
38D HIS 2.6 28.0 + - - -
39D ALA* 3.6 3.0 + - - -
40D LYS* 3.0 27.7 + - - -
55D PRO* 6.0 0.9 - - - +
172D LYS* 2.9 43.4 + - + +
173D VAL* 4.7 0.4 - - - +
174D ALA* 4.5 12.0 - - - +
203D TRP* 3.8 16.8 - - + -
205D ALA* 3.8 20.6 - - + -
317D ILE* 3.8 1.5 + - - -
318D SER* 1.3 76.5 - - - +
320D ASP* 1.3 65.6 + - - +
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Residues in contact with ASP 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.6 9.1 - - - +
38D HIS* 2.8 53.5 + - + +
40D LYS* 3.6 24.6 + - + +
145D LYS* 3.3 39.3 + - - +
172D LYS* 4.0 17.0 + - - +
319D THR* 1.3 80.0 + - - +
321D LYS* 1.3 71.6 + - - +
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Residues in contact with LYS 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 4.4 13.9 - - + -
36D ILE 3.4 6.1 - - - +
37D LEU* 3.7 18.6 - - + -
38D HIS* 4.4 1.6 - - - -
145D LYS* 3.2 33.3 + - - +
172D LYS* 3.9 23.7 - - - +
320D ASP* 1.3 79.4 + - - +
322D ALA* 1.3 63.8 + - - +
323D GLU* 3.8 28.5 + - - +
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Residues in contact with ALA 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 3.7 1.6 - - - +
36D ILE* 2.8 36.4 + - + +
38D HIS* 4.8 0.9 - - + -
143D LEU 3.6 24.2 - - - +
144D SER* 4.2 4.0 - - - -
145D LYS* 4.1 22.9 - - + +
321D LYS* 1.3 75.9 - - - +
323D GLU* 1.3 61.8 + - - +
324D TYR* 3.3 16.2 - - + +
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Residues in contact with GLU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D THR* 4.4 7.4 + - - +
34D VAL 4.2 3.6 - - - +
35D LEU* 3.8 38.5 - - + +
145D LYS* 5.7 0.6 - - - +
321D LYS* 3.8 30.8 + - - +
322D ALA* 1.3 71.6 - - - +
324D TYR* 1.3 82.3 + - - +
325D THR* 4.8 12.1 - - + +
342D VAL* 5.0 8.8 - - - +
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Residues in contact with TYR 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D THR* 3.4 3.0 - - - -
34D VAL* 3.3 30.9 + - + -
36D ILE* 4.8 1.1 - - + -
142D PHE* 3.8 31.9 - + + -
143D LEU* 2.6 48.2 + - - +
322D ALA* 3.3 21.8 - - + +
323D GLU* 1.3 94.8 - - - +
325D THR* 1.3 65.0 + - - +
326D PHE* 3.8 4.7 - - - -
340D VAL* 3.4 47.6 - - + -
342D VAL* 4.5 11.0 - - + -
363D ASN* 4.7 8.8 + - - -
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Residues in contact with THR 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ASP* 3.9 10.4 + - - +
32D GLN 3.8 6.5 - - - -
33D THR* 3.9 22.0 - - + +
323D GLU* 4.8 12.6 - - + +
324D TYR* 1.3 79.0 - - - +
326D PHE* 1.3 67.0 + - - +
340D VAL* 3.6 14.0 - - - +
422D TYR* 3.8 10.4 - - - +
423D SER* 3.5 33.2 + - - +
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Residues in contact with PHE 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ASP* 3.8 5.4 + - - -
32D GLN* 3.3 58.2 + - + +
33D THR* 4.1 8.5 - - - -
34D VAL 4.4 5.4 - - - -
66D TRP* 4.7 10.5 - + - -
131D MET* 5.8 0.4 - - + -
139D ILE* 5.3 6.5 - - + -
142D PHE* 4.4 18.8 - + - -
324D TYR 3.8 11.0 - - - -
325D THR* 1.3 84.3 + - - +
327D TYR* 1.3 59.3 + - - +
328D GLU* 5.9 3.6 - - + -
337D VAL* 3.3 46.9 - - + -
340D VAL* 4.9 4.5 - - + -
420D ILE* 4.4 4.9 - - + -
421D ILE 3.5 9.9 - - - -
422D TYR* 3.7 20.9 - + + -
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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