Contacts of the strand formed by residues 60 - 68 (chain B) in PDB entry 2CLS
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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.0 10.4 + - - +
12B ALA* 3.4 23.0 + - - +
53B CYS* 3.6 33.2 + - - +
54B LEU* 3.3 35.7 + - - +
55B GLU* 4.3 5.8 - - + +
59B GLN* 1.3 76.5 - - - +
61B VAL* 1.3 67.1 + - - +
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Residues in contact with VAL 61 (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 6.0 0.2 - - - -
12B ALA* 3.4 26.9 - - + +
14B CYS* 4.0 26.7 - - + -
52B ALA 3.7 0.7 - - - +
53B CYS* 3.4 6.0 - - - +
54B LEU* 2.7 45.1 + - + +
56B THR* 3.8 28.7 - - + -
59B GLN* 4.0 8.3 - - + -
60B ARG* 1.3 82.3 - - - +
62B GLU* 1.3 62.9 + - - +
63B LEU* 3.8 12.2 + - + -
184B SER* 4.4 7.6 - - - +
188B LEU* 5.8 2.9 - - + -
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Residues in contact with GLU 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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11B VAL 5.7 2.2 - - - +
12B ALA 2.6 16.1 + - - +
13B ARG* 3.5 13.5 - - + +
14B CYS 2.9 26.7 + - - -
51B THR* 5.6 6.3 - - + -
52B ALA 3.6 4.0 - - - -
53B CYS* 4.4 14.4 - - - -
61B VAL* 1.3 73.1 - - - +
63B LEU* 1.3 63.9 + - - +
64B SER* 3.8 0.5 + - - -
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Residues in contact with LEU 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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14B CYS* 3.4 31.4 - - + +
16B LEU* 4.3 7.2 - - + -
33B LEU* 4.5 5.8 - - + -
50B TYR 3.7 0.5 - - - +
51B THR* 3.3 11.9 - - - +
52B ALA* 2.6 41.5 + - + +
54B LEU* 3.7 33.0 - - + -
61B VAL* 4.0 4.9 - - + +
62B GLU* 1.3 72.5 - - - +
64B SER* 1.3 59.0 + - - +
65B LEU* 3.9 26.5 - - + -
180B PHE* 4.2 16.6 - - + -
184B SER* 3.2 24.2 - - - +
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Residues in contact with SER 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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13B ARG* 6.5 0.9 - - - -
14B CYS 2.9 13.5 + - - -
15B LYS* 3.4 8.7 - - - -
16B LEU 3.0 26.2 + - - +
49B ASN* 3.6 11.1 + - - -
50B TYR 3.6 4.0 - - - -
51B THR* 5.0 3.3 + - - +
62B GLU 3.8 1.2 + - - -
63B LEU* 1.3 71.0 - - - +
65B LEU* 1.3 61.0 + - - +
66B TRP* 3.4 24.3 + - - -
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Residues in contact with LEU 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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16B LEU* 3.5 19.1 - - + +
18B LEU* 4.8 1.6 - - + -
30B LEU* 4.2 16.8 - - + -
33B LEU* 3.7 22.0 - - + -
34B ALA* 5.0 1.6 - - + -
49B ASN* 2.8 9.0 + - - +
50B TYR* 2.8 61.0 + - + +
52B ALA* 3.8 22.0 - - + +
63B LEU* 4.0 17.0 - - + -
64B SER* 1.3 74.7 - - - +
66B TRP* 1.3 60.1 + - - +
67B ASP 3.9 0.9 + - - -
180B PHE* 3.8 32.3 - - + -
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Residues in contact with TRP 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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80A LEU* 4.6 10.3 - - + -
15B LYS* 3.6 37.4 - - + +
16B LEU 3.0 11.0 + - - +
17B VAL* 3.6 15.0 - - + +
18B LEU* 3.0 30.0 + - - +
30B LEU* 4.7 2.2 - - - -
47B PHE* 3.3 37.2 - + + -
48B GLU 3.7 4.5 - - - -
49B ASN* 3.7 13.2 - - + +
64B SER* 3.4 27.5 + - - -
65B LEU* 1.3 78.3 - - - +
67B ASP* 1.3 59.8 - - - +
80B LEU 4.9 2.0 - - - -
81B CYS* 3.5 32.5 - - + -
83B SER* 5.7 0.7 - - - -
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Residues in contact with ASP 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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18B LEU* 4.6 2.0 - - - +
26B LYS* 3.8 17.0 - - - +
27B THR* 2.6 39.5 + - - +
30B LEU* 3.7 22.2 - - + +
45B THR* 3.6 10.3 + - - +
47B PHE* 3.3 10.7 - - - -
48B GLU* 2.8 39.8 + - + +
50B TYR* 3.9 15.8 + - + -
65B LEU 3.9 0.8 + - - -
66B TRP* 1.3 70.9 - - - +
68B THR* 1.3 70.0 + - - +
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Residues in contact with THR 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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17B VAL* 4.0 19.5 - - + -
18B LEU 2.7 25.2 + - - +
19B VAL* 3.5 14.8 - - + +
26B LYS* 3.2 21.8 - - - -
45B THR* 4.1 6.9 - - - -
46B VAL 4.6 0.7 - - - -
47B PHE* 4.3 9.4 - - + -
66B TRP 4.5 0.7 - - - +
67B ASP* 1.3 83.9 + - - +
69B SER* 1.3 62.4 + - - +
78B ARG* 3.7 30.2 - - + -
81B CYS* 4.3 15.9 - - - -
500B GTP 3.9 1.7 + - - -
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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