Contacts of the strand formed by residues 397 - 406 (chain D) in PDB entry 2GVG
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 CYS 397 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D PHE* 3.6 15.9 - - + -
38D GLU 3.4 6.7 - - - -
39D CYS* 3.8 21.8 - - - +
153D VAL* 4.8 0.5 - - - +
156D TRP* 3.5 38.8 - - + -
159D ILE* 5.0 2.0 - - - -
160D THR* 4.0 9.2 - - - -
392D ARG* 3.0 41.6 + - + +
395D LEU* 4.0 14.6 - - - -
396D ASN* 1.3 74.3 - - - +
398D SER* 1.3 58.9 + - - +
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Residues in contact with SER 398 (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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36D TYR* 3.7 0.9 - - - +
37D PHE* 3.1 10.6 - - - -
38D GLU* 2.8 44.1 + - - +
40D ARG* 3.6 29.7 + - - -
153D VAL* 5.1 1.1 - - - -
392D ARG* 4.5 4.3 - - - +
396D ASN 3.2 2.9 + - - -
397D CYS* 1.3 75.0 - - - +
399D PHE* 1.3 58.3 + - - +
400D LYS* 2.5 41.4 + - - +
610D PO4 3.7 4.2 + - - -
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Residues in contact with PHE 399 (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 SER* 3.4 28.5 - - - -
36D TYR 3.2 12.3 - - - -
37D PHE* 4.5 3.1 - + + -
132D PHE* 4.1 18.4 - + - -
134D VAL* 3.6 30.3 - - + -
145D THR 4.0 13.0 - - - -
146D ASN* 3.7 15.0 + - - -
149D GLU* 3.2 57.5 + - + +
152D LEU* 4.3 9.0 - - + -
153D VAL* 3.4 22.5 - - + +
398D SER* 1.3 75.1 + - - +
400D LYS* 1.3 83.9 + - - +
610D PO4 4.7 1.2 + - - -
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Residues in contact with LYS 400 (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 SER* 3.1 6.6 - - - -
36D TYR* 2.9 59.6 + - + +
38D GLU* 5.6 2.0 - - + +
40D ARG* 5.1 1.9 - - - +
146D ASN* 5.8 0.4 - - - +
149D GLU* 4.8 1.3 + - - -
398D SER* 2.5 38.5 + - - +
399D PHE* 1.3 91.9 + - - +
401D CYS* 1.3 63.1 + - - +
415D LYS* 3.7 30.9 - - + +
423D LYS 5.6 0.4 - - - +
425D SER* 3.9 21.1 - - - +
610D PO4 2.7 28.9 + - - -
247E HIS* 5.3 5.2 - - + -
609E PO4 5.1 12.3 + - - -
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Residues in contact with CYS 401 (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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26D TYR* 5.7 0.2 - - - -
33D VAL* 4.0 13.2 - - + -
34D TYR 3.5 9.6 - - - -
35D SER* 3.3 14.5 + - - +
146D ASN* 4.7 1.6 - - - +
400D LYS* 1.3 76.4 - - - +
402D SER* 1.3 62.0 + - - +
403D TYR 3.9 0.7 - - - -
404D VAL* 3.5 30.7 - - - -
413D VAL* 3.5 23.5 - - + +
414D PHE* 4.3 5.9 + - - -
425D SER* 4.7 1.0 + - - -
248E SER* 3.6 32.8 - - - +
251E THR* 4.6 3.7 + - - +
252E ALA* 5.0 4.3 - - - -
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Residues in contact with SER 402 (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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34D TYR* 3.0 19.8 + - - -
36D TYR* 3.9 20.3 - - - -
400D LYS 3.6 0.8 + - - -
401D CYS* 1.3 74.5 - - - +
403D TYR* 1.3 61.2 + - - +
413D VAL* 2.8 25.3 + - - -
426D LYS 3.3 22.7 - - - -
428D GLY* 2.8 47.2 + - - -
430D LEU* 4.2 1.7 - - - +
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Residues in contact with TYR 403 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D LYS* 4.5 9.2 - - + -
34D TYR* 2.8 58.2 + + + +
402D SER* 1.3 82.2 + - - +
404D VAL* 1.3 68.0 + - - +
405D VAL* 3.7 21.0 - - + +
410D GLY* 3.4 35.8 - - - -
411D ILE 3.5 9.0 - - - -
412D ASN* 3.4 22.9 - - - -
413D VAL* 3.4 2.7 - - - +
428D GLY* 3.8 6.3 - - - -
429D ARG* 3.8 38.2 - - + -
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Residues in contact with VAL 404 (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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30D THR* 4.7 3.8 - - + -
32D LYS 3.0 15.5 - - - +
33D VAL* 4.4 9.0 - - + -
401D CYS* 3.5 21.8 - - - -
403D TYR* 1.3 83.8 - - - +
405D VAL* 1.3 62.9 + - - +
406D THR* 4.2 12.1 - - - +
409D LEU 3.7 0.2 - - - +
410D GLY* 3.3 2.8 - - - -
411D ILE* 2.7 57.5 + - + +
413D VAL* 4.1 4.9 - - + -
252E ALA* 3.5 33.0 - - + +
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Residues in contact with VAL 405 (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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30D THR* 3.3 3.6 - - - +
31D SER* 2.8 51.8 + - - +
32D LYS* 3.0 27.1 + - + -
403D TYR* 3.7 27.4 - - + +
404D VAL* 1.3 75.6 - - - +
406D THR* 1.3 59.8 + - - +
408D GLY* 3.9 28.3 - - - +
409D LEU 3.3 4.3 - - - +
410D GLY* 4.0 2.9 - - - -
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Residues in contact with THR 406 (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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27D PRO* 4.0 17.4 - - + +
28D PRO 3.5 22.2 - - - +
29D ASN 3.4 3.8 - - - +
30D THR* 2.7 21.5 + - - +
404D VAL* 4.1 13.7 - - - +
405D VAL* 1.3 72.4 - - - +
407D ASN* 1.3 87.7 - - - +
408D GLY 3.1 0.9 - - - -
409D LEU* 3.0 24.8 + - - +
411D ILE* 5.4 6.7 - - - -
252E ALA 4.8 0.6 + - - -
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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