Contacts of the strand formed by residues 75 - 86 (chain D) in PDB entry 2VKM
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 LYS 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D TYR* 3.7 29.4 + - + +
69D VAL 3.3 15.3 - - - +
70D PRO* 3.7 11.0 - - + -
71D TYR* 4.5 2.7 - - - +
74D GLY* 1.3 76.8 - - - +
76D TRP* 1.3 65.5 + - - +
105D SER* 3.4 0.7 - - - -
106D ASP* 2.9 61.9 + - + +
108D PHE* 3.8 6.7 - - - +
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Residues in contact with TRP 76 (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 ASN* 4.2 10.5 - - + -
39D ALA* 3.4 18.5 - - + +
67D VAL* 3.7 31.0 - - + -
68D TYR* 3.5 6.2 - - - -
69D VAL* 2.9 60.8 + - + +
71D TYR* 2.9 39.8 + + - -
75D LYS* 1.3 75.7 - - - +
77D GLU* 1.3 71.9 + - - +
78D GLY* 4.2 1.3 - - - -
100D ALA* 3.5 24.7 - - + -
102D ILE* 3.7 26.3 - - + +
104D GLU 3.4 12.3 - - - +
105D SER* 4.0 6.3 - - - +
108D PHE* 3.7 25.5 - + + -
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Residues in contact with GLU 77 (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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67D VAL 3.3 5.4 - - - +
68D TYR* 3.5 36.2 - - + +
76D TRP* 1.3 77.2 - - - +
78D GLY* 1.3 59.4 + - - +
102D ILE* 3.5 3.3 - - - -
103D THR* 2.9 24.5 + - - +
104D GLU* 2.9 32.9 + - + +
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Residues in contact with GLY 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D GLY* 3.4 5.0 - - - -
67D VAL* 2.8 43.0 + - - -
76D TRP* 4.0 3.0 - - - -
77D GLU* 1.3 77.0 - - - +
79D GLU* 1.3 65.0 + - - +
101D ALA 3.0 15.9 - - - -
102D ILE* 4.2 0.4 - - - -
103D THR* 3.8 7.4 - - - -
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Residues in contact with GLU 79 (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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54D ARG* 2.6 44.7 + - - +
60D TYR* 5.5 1.8 + - - +
62D ASP* 5.7 2.7 - - - +
65D LYS 3.7 7.0 - - - +
66D GLY* 5.4 2.7 - - - -
78D GLY* 1.3 79.0 - - - +
80D LEU* 1.3 65.9 + - - +
81D GLY 3.8 0.3 + - - -
99D ILE 3.6 1.0 - - - +
100D ALA* 4.4 1.1 - - - -
101D ALA* 2.8 38.0 + - - +
103D THR* 4.0 17.4 + - + +
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D TYR* 4.5 3.4 + - - -
62D ASP* 3.6 8.0 - - - +
63D LEU* 3.1 34.4 + - + +
64D ARG 4.0 1.7 + - - -
65D LYS* 2.8 51.5 + - + +
67D VAL* 3.8 25.1 - - + -
79D GLU* 1.3 75.1 - - - +
81D GLY* 1.3 59.1 + - - +
99D ILE 3.7 5.2 - - - +
100D ALA* 4.0 17.3 - - + +
129D PRO* 3.8 22.7 - - + -
133D LEU* 3.8 31.6 - - + -
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Residues in contact with GLY 81 (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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60D TYR* 4.2 10.5 - - - -
61D ARG 3.0 16.8 - - - -
63D LEU* 3.8 10.8 - - - +
79D GLU 3.8 0.2 + - - -
80D LEU* 1.3 75.8 - - - +
82D THR* 1.3 68.3 + - - +
98D ASN* 3.5 2.6 - - - +
99D ILE* 3.0 31.0 + - - -
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Residues in contact with THR 82 (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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60D TYR* 3.7 3.4 - - - -
61D ARG* 2.9 40.3 + - + +
63D LEU* 3.9 17.5 - - + -
81D GLY* 1.3 79.5 - - - +
83D ASP* 1.3 64.3 + - - +
96D ARG* 2.7 33.9 + - + -
97D ALA 3.1 14.1 - - - +
98D ASN* 3.6 19.7 - - - +
99D ILE* 4.5 2.2 - - - +
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Residues in contact with ASP 83 (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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21D GLY* 3.3 10.9 - - - +
52D TYR* 2.4 29.3 + - - +
57D SER* 2.7 23.6 + - - -
59D THR* 2.6 29.3 + - - -
60D TYR* 3.4 11.0 - - - -
82D THR* 1.3 76.2 - - - +
84D LEU* 1.3 79.3 + - - +
85D VAL* 3.6 3.8 - - - +
96D ARG* 3.2 9.5 - - - +
97D ALA 3.0 27.8 + - - -
99D ILE* 3.7 13.6 - - + +
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Residues in contact with LEU 84 (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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19D THR 4.5 0.2 - - - -
20D VAL* 3.2 4.5 - - - -
21D GLY 2.8 29.0 + - - +
22D SER* 4.0 9.9 - - - +
59D THR* 3.9 32.3 - - + +
83D ASP* 1.3 83.6 + - - +
85D VAL* 1.3 60.7 - - - +
94D THR* 3.8 21.1 - - + -
95D VAL 3.4 4.3 - - - +
96D ARG* 3.8 39.7 - - + +
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Residues in contact with VAL 85 (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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18D MET* 3.4 33.2 - - + -
19D THR 3.3 11.2 - - - +
20D VAL* 4.2 5.2 - - + -
38D PHE* 4.0 21.5 - - + -
83D ASP 3.6 11.9 - - - +
84D LEU* 1.3 81.6 - - - +
86D SER* 1.3 64.4 + - - +
93D VAL* 3.9 0.9 - - - +
94D THR* 3.3 4.3 - - - +
95D VAL* 2.7 40.3 + - - +
97D ALA* 4.2 9.4 - - + -
99D ILE* 4.1 12.3 - - + -
136D PHE* 3.8 15.0 - - + -
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Residues in contact with SER 86 (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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18D MET* 3.3 7.3 - - - +
19D THR* 2.9 44.7 + - - +
85D VAL* 1.3 72.6 - - - +
87D ILE* 1.3 69.0 + - - +
88D PRO* 4.0 3.8 - - - -
93D VAL* 3.3 11.6 + - - -
94D THR* 3.0 27.5 + - - +
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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