Contacts of the strand formed by residues 68 - 77 (chain B) in PDB entry 1EQR
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 CYS 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A PHE* 3.6 36.8 - - - -
524A GLY 3.1 30.1 - - - +
526A PRO* 3.8 13.5 - - - -
22B GLY 3.5 7.4 - - - -
23B TRP* 3.7 7.9 - - - +
66B GLU 3.5 1.4 + - - -
67B PHE* 1.3 72.1 - - - +
69B ILE* 1.3 61.0 + - - +
102B ILE* 2.8 31.3 + - - +
103B ASN* 2.9 21.1 + - + +
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Residues in contact with ILE 69 (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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21B CYS* 3.7 1.6 - - - -
22B GLY 2.9 31.8 + - - +
24B VAL* 4.2 14.8 - - + -
36B ILE* 5.8 2.0 - - + -
38B MET* 3.5 25.3 - - + +
49B PHE* 5.7 1.3 - - + -
63B LEU* 3.4 28.3 - - + -
67B PHE* 4.2 12.8 - - + +
68B CYS* 1.3 82.5 - - - +
70B GLN* 1.3 58.7 + - - +
71B VAL* 3.3 26.9 - - + -
99B LEU* 4.0 4.7 - - + -
100B THR 3.3 6.1 - - - +
101B ILE* 3.4 25.8 - - + -
102B ILE* 3.7 7.0 - - - +
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Residues in contact with GLN 70 (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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1B MET* 3.5 15.6 + - - +
19B THR* 3.8 21.3 - - + +
20B LEU 3.3 9.2 - - - +
21B CYS* 3.3 22.2 - - - +
69B ILE* 1.3 73.4 - - - +
71B VAL* 1.3 69.3 + - - +
72B THR* 4.9 8.2 - - + +
99B LEU* 3.6 0.3 - - - -
100B THR* 2.7 57.2 + - + +
102B ILE* 3.6 17.0 - - + +
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Residues in contact with VAL 71 (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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18B VAL 4.2 0.2 - - - +
19B THR* 3.6 0.7 - - - +
20B LEU* 2.8 39.5 + - + +
38B MET* 4.1 15.5 - - + -
47B VAL* 4.1 21.5 - - + -
49B PHE* 4.3 9.9 - - + -
69B ILE* 3.3 27.1 - - + -
70B GLN* 1.3 81.7 - - - +
72B THR* 1.3 68.5 + - - +
73B GLY 4.3 1.7 + - - +
94B VAL* 5.1 2.5 - - + -
96B ALA* 4.6 7.2 - - + -
98B SER 3.1 13.9 - - - +
99B LEU* 3.7 12.1 - - + -
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Residues in contact with THR 72 (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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17B GLN* 4.0 17.8 + - - -
18B VAL 3.0 15.2 + - - -
19B THR* 3.4 22.6 + - + +
70B GLN* 4.9 9.4 - - + +
71B VAL* 1.3 78.4 - - - +
73B GLY* 1.3 57.0 + - - +
97B SER* 2.8 27.1 + - - -
98B SER* 3.0 34.4 + - - +
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Residues in contact with GLY 73 (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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17B GLN* 3.3 4.8 - - - -
18B VAL* 2.6 41.0 + - - +
71B VAL 4.2 1.0 + - - -
72B THR* 1.3 74.2 - - - +
74B THR* 1.3 60.4 + - - -
94B VAL* 4.1 12.6 - - - +
95B LEU 3.0 18.6 - - - -
96B ALA* 3.9 1.1 - - - -
97B SER* 3.5 9.2 - - - -
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Residues in contact with THR 74 (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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15B GLY* 3.8 20.6 - - - +
16B GLN 3.4 13.7 - - - +
17B GLN* 3.9 15.5 + - + +
73B GLY* 1.3 73.6 - - - -
75B VAL* 1.3 76.1 + - - +
76B ARG* 3.9 1.4 + - - +
94B VAL* 3.6 2.2 - - - -
95B LEU* 2.8 39.7 + - - +
97B SER* 4.9 1.2 + - - -
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Residues in contact with VAL 75 (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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9B LEU* 4.5 8.7 - - + -
10B ARG 4.3 0.7 - - - +
13B HIS* 3.5 29.4 - - + +
14B VAL* 3.5 24.2 - - + +
15B GLY* 3.0 21.7 + - - -
16B GLN 3.0 14.3 + - - +
18B VAL* 4.1 15.3 - - + -
74B THR* 1.3 77.9 - - - +
76B ARG* 1.3 68.5 - - - +
92B ILE* 4.2 17.9 - - + -
93B GLU 3.7 9.0 - - - +
94B VAL* 4.0 17.7 - - + -
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Residues in contact with ARG 76 (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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14B VAL* 3.9 11.4 - - + -
48B PHE* 3.2 34.4 - - - +
74B THR 4.7 2.7 - - - +
75B VAL* 1.3 79.5 - - - +
77B ALA* 1.3 65.2 + - - +
92B ILE* 3.3 10.3 - - - +
93B GLU* 2.7 64.2 + - + +
95B LEU* 3.5 36.9 - - + +
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Residues in contact with ALA 77 (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 LEU* 4.6 9.9 - - + -
14B VAL* 4.2 10.7 - - + +
76B ARG* 1.3 83.1 + - - +
78B ARG* 1.3 68.5 + - - +
79B ASP* 3.6 4.2 + - - +
80B GLU* 5.3 4.9 - - - +
83B ILE* 6.5 0.2 - - + -
91B GLU 3.6 9.9 - - - +
92B ILE* 4.1 3.1 - - - -
93B GLU* 4.6 2.7 - - - +
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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