Contacts of the strand formed by residues 89 - 105 (chain B) in PDB entry 2VWE
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 GLN 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B VAL* 5.7 0.7 - - - +
81B LEU* 3.8 6.0 - - - +
82B MET* 2.8 62.2 + - + +
84B ARG* 5.4 12.9 + - + -
87B SER* 3.5 8.7 + - - +
88B SER* 1.3 75.5 + - - +
90B LEU* 1.3 60.6 + - - +
91B GLY* 3.5 5.1 + - - +
30C SER 5.9 1.3 - - - +
32C PHE* 4.7 1.1 - - + -
50C TYR* 3.9 9.0 - - - +
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Residues in contact with LEU 90 (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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17A TRP* 3.5 46.7 - - + -
79B GLN* 3.5 38.3 + - + +
80B ILE 3.6 5.4 - - - -
81B LEU* 3.6 32.7 - - + +
89B GLN* 1.3 70.9 + - - +
91B GLY* 1.3 58.9 + - - +
32C PHE* 5.3 0.4 - - - -
49C TYR* 4.2 6.5 - - + -
50C TYR* 3.1 52.7 + - + -
100E VAL* 5.1 2.0 - - + -
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Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLN* 3.4 12.8 - - - +
80B ILE* 2.8 35.9 + - - +
82B MET* 3.8 20.0 - - - +
89B GLN* 3.5 8.3 + - - -
90B LEU* 1.3 72.0 - - - +
92B GLU* 1.3 60.7 + - - -
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.4 19.7 - - + +
77B ARG* 2.8 49.4 + - + +
78B MET 3.6 13.7 - - - +
79B GLN* 4.5 2.2 - - + +
80B ILE* 4.4 3.5 - - - +
82B MET* 4.7 8.4 - - - +
91B GLY* 1.3 75.4 - - - +
93B MET* 1.3 69.7 + - - +
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Residues in contact with MET 93 (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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35B LEU* 3.8 3.8 - - + -
40B MET* 3.7 34.5 - - + +
47B LEU* 5.5 0.7 - - + -
52B VAL* 3.5 43.3 - - + -
77B ARG* 3.1 8.9 - - - +
78B MET* 2.8 54.4 + - + +
80B ILE* 3.8 31.2 - - + +
92B GLU* 1.3 75.9 - - - +
94B SER* 1.3 61.7 + - - +
95B LEU* 3.8 15.7 - - + -
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Residues in contact with SER 94 (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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40B MET* 5.3 5.5 - - - +
75B GLN* 5.4 10.6 + - - -
76B VAL 3.4 10.8 - - - -
77B ARG* 4.4 8.1 - - - -
78B MET 4.8 0.4 - - - +
93B MET* 1.3 78.8 - - - +
95B LEU* 1.3 74.0 + - - +
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Residues in contact with LEU 95 (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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33B VAL* 4.0 28.7 - - + -
35B LEU* 4.0 11.7 - - + -
39B LEU* 5.1 7.2 - - + -
40B MET* 4.3 14.4 - - + -
52B VAL* 4.1 14.6 - - + -
54B VAL* 4.5 11.4 - - + -
56B ARG* 4.1 14.1 - - - +
75B GLN* 3.5 6.2 - - - -
76B VAL* 3.0 34.4 + - - +
78B MET* 4.5 11.1 - - + +
93B MET* 3.8 24.9 - - + -
94B SER* 1.3 87.1 - - - +
96B GLU* 1.3 62.8 + - - +
97B GLU 3.5 0.3 + - - -
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Residues in contact with GLU 96 (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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54B VAL* 4.6 2.3 - - - +
56B ARG* 3.0 32.5 + - - +
73B GLN* 3.9 35.7 + - + +
75B GLN* 3.8 34.9 + - + +
95B LEU* 1.3 72.6 - - - +
97B GLU* 1.3 61.0 + - - +
98B HIS* 4.5 9.2 + - + -
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Residues in contact with GLU 97 (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 THR 5.0 0.7 - - - +
54B VAL* 3.9 12.6 - - + +
55B GLN* 3.3 51.0 + - + +
56B ARG* 4.6 0.9 - - - +
73B GLN* 3.3 3.9 - - - +
74B HIS* 2.8 70.0 + - + +
76B VAL* 3.4 30.5 - - + +
95B LEU 3.5 0.8 + - - -
96B GLU* 1.3 74.7 - - - +
98B HIS* 1.3 63.4 + - - +
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Residues in contact with HIS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PRO* 4.8 3.9 - - + +
55B GLN* 2.9 30.6 + - - +
56B ARG* 3.5 30.4 + - + -
57B CYS* 3.3 46.4 + - + +
70B PRO* 3.4 29.9 - - + +
72B GLY 4.6 2.0 - - - +
73B GLN* 3.9 14.1 + - + +
74B HIS* 4.6 3.9 - - - -
96B GLU* 4.5 11.1 + - + -
97B GLU* 1.3 81.7 - - - +
99B SER* 1.3 62.1 + - - +
101B CYS* 5.2 0.2 - - - -
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Residues in contact with SER 99 (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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28B PRO* 3.4 17.2 - - - +
72B GLY* 2.9 22.5 + - - -
73B GLN* 3.7 8.3 - - - -
74B HIS* 3.0 28.8 + - - +
98B HIS* 1.3 72.6 - - - +
100B GLN* 1.3 62.7 + - - +
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Residues in contact with GLN 100 (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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28B PRO* 3.9 9.4 - - + -
57B CYS* 4.1 0.7 - - - -
70B PRO* 3.7 3.3 - - - +
71B THR* 2.7 39.8 + - - +
72B GLY 3.4 4.8 + - - +
98B HIS 4.0 0.2 - - - -
99B SER* 1.3 82.4 - - - +
101B CYS* 1.3 73.1 + - - +
102B GLU* 5.5 7.1 + - - +
27L TYR 5.0 9.3 + - - -
28L THR* 5.4 7.1 - - + +
29L PHE* 5.4 3.2 - - - +
76L SER* 4.6 12.3 + - - -
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Residues in contact with CYS 101 (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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26B CYS* 3.6 23.6 - - - +
27B GLN* 3.6 2.7 - - - -
28B PRO* 3.5 28.0 - - - +
57B CYS* 2.0 53.6 - - + -
69B VAL 3.7 7.0 - - - +
71B THR* 4.3 1.3 - - - +
100B GLN* 1.3 85.5 + - - +
102B GLU* 1.3 68.7 + - - +
28L THR* 3.4 18.9 + - - +
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Residues in contact with GLU 102 (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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26B CYS* 4.6 3.6 - - - -
67B GLU 3.5 0.2 - - - +
68B CYS* 4.1 1.2 - - - -
69B VAL* 3.1 33.2 + - - +
71B THR* 3.7 24.9 - - + +
100B GLN* 5.5 7.3 + - + +
101B CYS* 1.3 80.2 - - - +
103B CYS* 1.3 62.3 + - - +
104B ARG* 3.5 17.3 + - + -
28L THR* 4.5 2.9 - - + -
29L PHE 6.3 0.2 - - - +
30L THR* 3.3 26.7 - - + +
73L LYS* 2.6 60.8 + - - +
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Residues in contact with CYS 103 (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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25B THR* 5.6 1.1 - - - -
26B CYS* 3.8 18.6 - - - -
61B CYS* 2.0 51.1 - - + -
62B PRO* 4.4 7.6 - - + -
66B LEU* 3.4 17.6 - - + +
67B GLU 3.5 4.0 - - - -
102B GLU* 1.3 71.5 - - - +
104B ARG* 1.3 60.3 + - - +
28L THR* 5.2 2.2 - - - +
30L THR* 3.2 24.1 + - - +
31L GLY* 5.0 4.5 - - - -
53L GLY* 3.4 23.2 - - - +
73L LYS* 4.8 1.2 + - - -
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Residues in contact with ARG 104 (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 LEU* 4.0 2.2 - - - -
67B GLU* 2.6 43.1 + - + +
69B VAL* 3.8 27.7 - - + +
70B PRO 5.2 3.0 + - - -
71B THR* 3.4 34.5 - - - +
102B GLU* 3.5 13.8 + - - +
103B CYS* 1.3 76.8 - - - +
105B PRO* 1.3 70.1 - - + +
53L GLY 4.8 0.2 - - - -
73L LYS* 3.7 29.1 - - - +
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Residues in contact with PRO 105 (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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65B GLY 3.3 12.6 - - - +
66B LEU* 3.9 7.6 - - + -
67B GLU* 4.7 2.8 - - - +
103B CYS 4.3 0.7 - - - +
104B ARG* 1.3 88.8 - - + +
106B LYS* 1.3 65.5 + - - +
107B LYS* 3.3 6.4 + - - +
53L GLY 4.1 11.4 - - - +
54L ASN* 4.4 24.5 - - + +
73L LYS* 6.2 0.2 - - - +
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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