Contacts of the strand formed by residues 61 - 68 (chain B) in PDB entry 1EVW
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 ARG 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LYS* 3.3 2.6 - - - -
57B ASN* 2.7 31.0 + - - +
58B GLY* 2.7 32.9 + - - +
60B THR* 1.3 92.6 + - - +
62B TRP* 1.3 73.5 + - - +
76B GLY* 6.0 1.8 - - - -
77B SER* 6.1 0.9 - - - -
78B HIS* 4.9 13.7 + - - -
98B HIS* 5.9 2.2 - - - -
103B THR* 5.2 5.9 - - - +
13E A 5.2 2.4 + - - -
14M G 3.3 46.7 + - - +
15M A 3.0 82.1 + - - +
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Residues in contact with TRP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE* 3.6 36.7 - - + +
45B PRO 4.9 2.1 + - - -
50B TYR* 4.7 7.4 - + - -
54B PHE* 5.2 0.2 - - + -
55B ALA 2.9 11.4 - - - +
56B LYS* 3.6 31.0 - - + +
57B ASN* 2.7 12.2 + - - +
59B PRO 4.4 3.6 - - - -
60B THR* 3.6 30.1 - - + -
61B ARG* 1.3 93.3 + - - +
63B GLN* 1.3 65.7 + - - +
76B GLY* 3.9 2.9 - - - -
77B SER* 3.0 45.2 + - - +
78B HIS* 3.7 8.3 - + - -
103B THR* 3.5 24.0 - - + -
104B ARG* 3.6 33.2 - - + -
106B HIS* 3.8 11.2 - + - -
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Residues in contact with GLN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLY 3.4 4.3 - - - +
54B PHE* 3.4 5.2 - - - -
55B ALA* 2.8 36.5 + - + +
57B ASN* 3.0 26.0 + - - +
62B TRP* 1.3 81.5 - - - +
64B TYR* 1.3 60.7 + - - +
65B LYS* 5.3 0.5 - - - +
74B ARG* 3.6 32.5 + - + +
75B TRP 3.3 15.6 - - - +
76B GLY* 4.6 2.0 - - - -
77B SER 3.8 2.0 - - - +
4F C 5.1 2.1 + - - -
16M G 3.8 12.9 + - - +
17M A 2.8 48.4 + - - -
18M G 4.9 0.3 - - - +
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Residues in contact with TYR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.0 15.0 - - + -
14B SER* 3.3 25.4 + - - -
15B TRP* 3.3 37.7 + + + -
18B THR* 4.3 2.6 + - - -
52B VAL 3.2 23.4 + - - -
53B GLY* 3.3 12.8 - - - -
54B PHE* 3.6 34.8 - + + -
63B GLN* 1.3 73.2 - - - +
65B LYS* 1.3 60.6 + - - +
66B ARG* 3.7 35.2 + - + -
74B ARG* 3.2 3.7 - - - +
75B TRP* 2.8 40.0 + + + +
77B SER* 4.1 4.5 - - - +
80B VAL* 4.1 16.6 - - + -
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLY* 2.9 24.0 + - - +
55B ALA* 5.8 6.2 - - - +
63B GLN 5.3 0.7 - - - +
64B TYR* 1.3 76.4 - - - +
66B ARG* 1.3 73.5 + - - +
72B VAL* 3.5 30.1 - - + -
73B HIS 3.2 8.3 - - - +
74B ARG* 3.9 25.8 - - + +
1F T 3.4 47.4 + - + +
2F G 3.0 38.6 + - - -
3F A 4.8 8.1 + - - +
19M T 6.0 0.7 - - - -
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.2 6.7 - - + +
14B SER* 3.7 29.3 - - - -
52B VAL* 3.8 29.0 + - - +
64B TYR* 3.7 36.4 + - + -
65B LYS* 1.3 83.3 + - - +
67B THR* 1.3 62.1 + - - +
68B ILE* 3.9 17.4 + - + +
72B VAL* 4.5 1.8 - - - -
73B HIS* 2.8 35.2 + - - +
75B TRP* 4.2 12.5 - - + -
1F T 4.0 21.2 + - - -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG* 1.3 74.3 - - - +
68B ILE* 1.3 68.5 - - - +
69B ASN 4.3 0.2 - - - -
70B GLN* 4.4 9.0 - - - +
71B VAL 3.5 24.2 - - - +
72B VAL* 3.9 11.6 - - + +
1F T 3.6 33.9 + - + +
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 3.8 28.5 - - + -
7B GLN* 3.2 34.5 - - + +
10B ALA* 6.4 0.4 - - + -
11B VAL* 4.2 25.1 - - + -
66B ARG* 3.9 18.6 + - + +
67B THR* 1.3 79.9 - - - +
69B ASN* 1.3 77.5 + - + +
70B GLN 3.2 0.4 - - - -
71B VAL* 2.9 30.4 + - - +
73B HIS* 5.1 4.0 - - - +
75B TRP* 5.1 3.1 - - + -
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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