Contacts of the strand formed by residues 30 - 39 (chain E) 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 THR 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E TYR* 4.4 8.1 - - + -
27E PRO* 2.7 33.7 + - - +
28E PRO 3.2 0.2 - - - -
29E ASN* 1.3 75.9 - - - +
31E SER* 1.3 58.8 + - - +
32E LYS 3.9 7.2 - - - +
33E VAL* 4.2 14.6 - - + -
139E PRO 4.0 1.2 - - - +
142E TYR* 3.2 39.1 - - + +
404E VAL* 3.7 20.2 - - + -
405E VAL 3.3 11.9 - - - +
406E THR* 3.0 14.0 + - - +
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Residues in contact with SER 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ASN 3.6 4.5 + - - -
30E THR* 1.3 74.7 - - - +
32E LYS* 1.3 60.4 - - - +
136E ASN* 2.9 19.9 - - - +
139E PRO* 3.4 34.0 - - - +
142E TYR* 4.1 2.9 - - - -
405E VAL* 2.9 28.8 + - - +
408E GLY* 5.3 1.7 + - - -
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Residues in contact with LYS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E THR* 3.6 1.3 - - - +
31E SER* 1.3 83.3 + - - +
33E VAL* 1.3 72.5 + - - +
34E TYR* 4.5 2.5 - - + +
135E GLU* 3.3 31.7 + - + +
136E ASN* 3.5 25.3 + - - +
137E THR* 5.4 1.0 - - - +
403E TYR* 4.4 19.1 - - + -
404E VAL* 3.3 13.2 - - - +
405E VAL* 3.1 49.1 + - + +
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Residues in contact with VAL 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E TYR* 3.9 32.5 - - + +
30E THR* 4.2 6.7 - - + -
32E LYS* 1.3 79.0 - - - +
34E TYR* 1.3 60.9 + - - +
35E SER* 4.2 0.7 - - - +
135E GLU* 3.5 5.7 - - - -
136E ASN* 2.9 12.4 + - - +
142E TYR* 3.1 34.8 - - + +
145E THR* 2.8 39.1 + - + +
146E ASN* 3.9 15.3 - - - +
401E CYS* 4.1 16.4 - - - -
403E TYR 3.8 2.7 - - - -
404E VAL* 4.6 3.1 - - + -
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Residues in contact with TYR 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LYS* 4.6 3.4 - - + -
33E VAL* 1.3 73.7 - - - +
35E SER* 1.3 66.6 + - - +
117E LYS* 6.2 1.3 - - + -
133E THR* 3.4 35.9 + - + +
134E VAL 3.4 6.1 - - - -
135E GLU* 3.6 36.8 - - + -
401E CYS* 3.6 2.3 - - - -
402E SER* 3.0 46.4 + - - -
403E TYR* 2.8 41.3 + + + +
429E ARG* 3.7 24.5 - - + +
430E LEU* 2.9 35.6 + - + -
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Residues in contact with SER 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 4.2 0.7 - - - +
34E TYR* 1.3 77.1 - - - +
36E TYR* 1.3 62.8 + - - +
133E THR* 3.2 6.4 - - - -
134E VAL* 2.8 32.3 + - - +
145E THR* 3.7 6.5 - - - +
146E ASN* 2.7 22.6 + - - -
399E PHE* 3.3 32.7 - - - -
400E LYS 3.2 10.8 - - - -
401E CYS* 3.3 15.1 - - - +
402E SER 4.3 0.7 - - - +
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Residues in contact with TYR 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E TYR* 5.1 0.4 - - + -
35E SER* 1.3 75.8 - - - +
37E PHE* 1.3 68.7 + - - +
38E GLU* 2.8 45.4 + - + -
130E VAL* 4.0 4.9 - - + -
132E PHE* 3.3 12.1 - - - +
133E THR* 3.9 9.0 - - + +
398E SER 3.8 0.7 - - - +
399E PHE* 3.3 8.6 - - - -
400E LYS* 2.8 68.9 + - + +
402E SER* 3.8 18.8 - - - +
425E SER* 3.4 8.2 - - - -
426E LYS* 2.9 45.0 + - + +
430E LEU* 3.4 27.4 - - + -
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Residues in contact with PHE 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E TYR* 1.3 75.8 - - - +
38E GLU* 1.3 63.8 + - - +
39E CYS* 4.2 7.0 - - - -
130E VAL* 3.7 2.9 - - - -
131E LEU* 2.9 46.2 + - + -
132E PHE* 2.9 51.4 + + + +
153E VAL* 4.3 20.2 - - + -
155E SER* 3.7 18.2 - - - -
156E TRP* 4.5 2.5 - - - -
159E ILE* 3.7 25.6 - - + -
397E CYS* 3.7 31.9 - - + -
398E SER 3.3 19.7 - - - -
399E PHE* 4.7 6.7 - - + -
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Residues in contact with GLU 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E TYR* 2.8 39.8 + - + -
37E PHE* 1.3 79.5 - - - +
39E CYS* 1.3 62.1 + - - +
40E ARG* 3.8 35.3 + - + +
128E GLY* 3.8 6.8 - - - -
129E ASN 3.4 20.6 - - - +
131E LEU* 4.5 1.1 - - - -
396E ASN 3.4 1.2 - - - +
397E CYS* 3.5 1.9 - - - -
398E SER* 3.0 41.4 + - - +
400E LYS* 5.5 2.3 - - + +
424E ARG 4.6 7.6 - - - +
425E SER* 4.6 0.9 - - - -
426E LYS* 3.3 21.2 + - - +
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Residues in contact with CYS 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E PHE* 4.2 5.2 - - - -
38E GLU* 1.3 71.5 - - - +
40E ARG* 1.3 69.5 + - - +
57E THR* 4.0 20.4 - - + +
127E ARG* 3.2 21.1 - - + +
128E GLY 3.0 19.1 + - - +
129E ASN 4.3 4.4 + - - +
131E LEU* 3.8 23.1 - - + +
159E ILE* 4.3 9.4 - - - -
395E LEU* 3.2 18.2 - - - +
396E ASN 3.7 1.1 - - - -
397E CYS* 3.7 24.9 - - - -
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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