Contacts of the strand formed by residues 61 - 67 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D LYS* 2.9 13.2 - - - +
57D ASN* 2.6 26.3 + - - +
58D GLY* 2.9 30.4 + - - +
59D PRO* 5.9 0.4 - - + -
60D THR* 1.3 93.1 + - - +
62D TRP* 1.3 64.6 + - - +
76D GLY* 5.8 2.2 - - - -
77D SER* 6.0 0.4 - - - -
78D HIS* 4.5 15.5 + - - -
98D HIS* 6.0 0.4 - - - -
103D THR* 5.1 5.5 - - - +
13G A 5.5 0.2 + - - -
14N G 3.6 49.3 + - - -
15N A 2.4 84.8 + - - +
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Residues in contact with TRP 62 (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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44D ILE* 3.5 40.3 - - + +
45D PRO 4.7 2.8 + - - -
46D LEU 5.8 0.2 + - - -
50D TYR* 4.5 13.0 - + - -
54D PHE* 5.1 0.7 - - + -
55D ALA 2.9 16.4 - - - +
56D LYS* 3.2 29.7 - - + +
57D ASN* 2.9 7.1 + - - +
59D PRO 4.5 4.9 + - - -
60D THR* 3.6 33.2 - - + -
61D ARG* 1.3 80.9 + - - +
63D GLN* 1.3 69.1 + - - +
76D GLY* 4.0 2.9 - - - -
77D SER* 3.1 43.0 + - - +
78D HIS* 3.8 11.9 - + - -
103D THR* 3.8 20.9 - - + -
104D ARG* 3.7 31.4 - - + -
106D HIS* 3.9 4.9 - + - -
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Residues in contact with GLN 63 (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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53D GLY 3.3 5.7 - - - +
54D PHE* 3.3 6.5 - - - -
55D ALA* 2.8 34.7 + - + +
57D ASN* 3.5 20.5 - - - +
62D TRP* 1.3 81.4 - - - +
64D TYR* 1.3 59.9 + - - +
65D LYS* 4.1 0.6 + - - +
74D ARG* 3.7 29.9 + - + +
75D TRP 3.2 14.9 - - - +
76D GLY* 4.9 1.3 - - - -
77D SER 3.9 2.9 - - - +
4H C 5.1 3.8 - - - +
16N G 3.4 16.7 + - - +
17N A 2.7 50.2 - - - +
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Residues in contact with TYR 64 (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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11D VAL* 3.9 16.4 - - + -
14D SER* 3.2 25.1 + - - -
15D TRP* 3.5 35.4 + + + +
18D THR* 4.4 2.7 + - - -
52D VAL 3.2 23.8 + - - -
53D GLY* 3.5 12.3 - - - -
54D PHE* 3.5 34.5 - + + -
63D GLN* 1.3 72.3 - - - +
65D LYS* 1.3 60.6 + - - +
66D ARG* 3.6 33.8 + - + -
74D ARG* 3.3 2.8 - - - -
75D TRP* 2.8 42.3 + + + +
77D SER* 4.2 3.7 - - - +
80D VAL* 4.0 16.2 - - + -
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Residues in contact with LYS 65 (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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53D GLY* 2.9 22.6 + - - +
63D GLN 5.4 0.2 - - - +
64D TYR* 1.3 76.1 - - - +
66D ARG* 1.3 74.9 + - - +
72D VAL* 3.6 18.8 - - + -
73D HIS 3.1 6.7 - - - +
74D ARG* 3.6 29.8 - - + +
1H T 3.3 52.8 + - + +
2H G 2.7 45.0 + - - -
3H A 4.7 8.2 + - - +
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Residues in contact with ARG 66 (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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11D VAL* 4.2 9.2 - - + +
14D SER* 3.9 24.5 - - - -
52D VAL* 4.0 22.4 + - - +
64D TYR* 3.6 37.7 + - + -
65D LYS* 1.3 80.4 + - - +
67D THR* 1.3 59.6 + - - +
68D ILE* 3.9 18.1 + - + +
71D VAL 3.8 0.3 - - - +
72D VAL* 4.5 2.7 - - - -
73D HIS* 2.7 44.3 + - - +
75D TRP* 4.1 8.4 - - + -
1H T 3.5 26.0 + - - -
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Residues in contact with THR 67 (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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66D ARG* 1.3 73.7 - - - +
68D ILE* 1.3 68.3 + - - +
69D ASN 4.3 0.4 - - - -
70D GLN* 4.3 9.4 - - - +
71D VAL 3.4 24.5 - - - +
72D VAL* 4.1 7.9 - - + +
1H T 3.0 39.9 + - + +
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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