Contacts of the strand formed by residues 23 - 31 (chain B) in PDB entry 1C1D
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 ALA 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.5 3.2 - - - -
18B ASP 3.0 27.2 + - - -
21B THR* 3.1 16.7 + - - +
22B GLY* 1.3 80.0 - - - +
24B HIS* 1.4 61.6 + - - +
25B PHE* 3.6 19.4 - - + -
81B ILE* 4.5 5.8 - - + -
82B ALA 3.6 10.1 - - - +
84B PRO* 4.4 5.4 - - + -
98B ILE* 3.9 23.1 - - + -
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Residues in contact with HIS 24 (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 THR* 6.4 0.2 - - - -
16B ARG 3.5 5.4 + - - -
17B PHE* 3.2 48.4 - + + +
22B GLY 4.4 4.3 - - - -
23B ALA* 1.4 73.2 - - - +
25B PHE* 1.3 62.6 + - - +
26B VAL* 5.4 0.9 - - + -
49B LEU* 3.2 48.8 - - + +
80B VAL 4.1 0.4 - - - +
81B ILE* 3.5 6.8 - - - +
82B ALA* 2.9 42.8 + - + +
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 5.2 0.7 - - + -
15B THR* 3.2 8.1 - - - -
16B ARG* 2.9 44.3 + - + +
18B ASP* 4.0 11.4 - - + -
23B ALA* 3.6 33.0 - - + -
24B HIS* 1.3 77.0 - - - +
26B VAL* 1.3 65.9 + - - +
27B ILE* 6.0 1.6 - - + -
80B VAL 3.8 2.9 - - - -
81B ILE* 4.1 12.3 - - + -
98B ILE* 3.3 41.3 - - + -
101B ILE* 3.5 28.0 - - + -
102B HIS* 3.8 24.0 - - + +
105B ASN* 3.8 21.3 - - - +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B THR* 4.4 1.3 - - + -
14B VAL 3.3 7.2 - - - +
15B THR* 4.3 4.0 - - + -
24B HIS* 5.4 1.6 - - + -
25B PHE* 1.3 81.5 - - - +
27B ILE* 1.3 73.9 + - - +
28B ARG* 4.2 6.7 - - + -
49B LEU* 4.6 9.2 - - + -
52B ALA* 4.5 17.5 - - + -
53B LEU* 3.8 35.7 - - + +
56B ALA* 3.6 28.0 - - + -
78B LYS 4.0 0.2 - - - +
79B SER* 3.2 4.5 - - - -
80B VAL* 2.8 41.5 + - + +
82B ALA* 6.1 0.4 - - + -
102B HIS* 5.4 0.2 - - - -
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Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B MET 3.8 0.5 - - - +
13B THR* 3.4 2.6 - - - +
14B VAL* 2.7 51.7 + - + +
25B PHE* 5.8 1.3 - - + -
26B VAL* 1.3 77.6 - - - +
28B ARG* 1.4 63.8 + - - +
29B LEU* 3.8 24.6 - - + +
78B LYS 3.5 10.1 - - - +
79B SER* 3.6 11.2 - - - +
102B HIS* 4.2 7.2 - - + +
105B ASN* 4.1 26.5 - - + +
106B ILE* 4.1 22.2 - - + +
109B LEU* 4.1 20.6 - - + -
113B TYR* 3.8 17.7 - - + -
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Residues in contact with ARG 28 (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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4B SER 3.0 22.2 + - - -
5B ALA 2.7 24.5 + - - -
6B LEU* 4.7 2.0 + - - +
8B TRP* 3.3 38.1 - - + +
12B MET 3.4 0.9 - - - -
13B THR* 2.7 36.9 + - + +
26B VAL* 4.2 6.8 - - + +
27B ILE* 1.4 76.2 - - - +
29B LEU* 1.3 64.6 + - - +
30B ASP 3.8 0.7 - - - -
53B LEU* 2.9 33.4 + - - +
56B ALA* 3.9 19.5 - - + +
57B GLY* 3.5 22.2 - - - +
60B ALA* 3.5 2.4 - - + +
77B GLY* 3.0 4.5 - - - -
78B LYS 2.8 33.4 + - - +
860B IPA 3.5 13.7 + - - -
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Residues in contact with LEU 29 (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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8B TRP* 3.4 2.7 - - - -
11B GLU* 3.0 28.3 + - + +
12B MET* 2.8 41.0 + - + +
14B VAL* 5.8 0.4 - - + -
27B ILE* 3.8 11.9 - - + +
28B ARG* 1.3 76.3 - - - +
30B ASP* 1.3 61.6 + - - +
31B SER 3.4 0.4 - - - -
32B THR* 4.8 9.0 - - + -
37B ALA* 3.8 12.3 - - + -
76B GLY 3.8 3.8 - - - -
109B LEU* 4.4 11.7 - - + -
112B ASN* 3.9 28.7 - - + +
113B TYR* 3.6 39.7 - - + -
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Residues in contact with ASP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TRP* 3.6 25.7 + - + -
9B ASP* 4.6 4.9 - - - +
10B GLY* 3.7 4.3 - - - -
11B GLU* 3.2 10.8 + - - +
28B ARG 3.8 2.4 + - - -
29B LEU* 1.3 73.0 - - - +
31B SER* 1.3 55.7 + - - +
60B ALA* 3.6 21.1 - - + +
61B GLY* 3.6 15.7 - - - -
64B THR* 2.7 32.9 + - - +
76B GLY 2.8 11.9 + - - +
854B NA 2.6 30.5 - - - -
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 3.4 9.2 + - - -
29B LEU 3.4 0.6 - - - -
30B ASP* 1.3 88.2 - - - +
32B THR* 1.4 69.2 + - - +
33B GLN* 3.1 23.9 + - - +
34B LEU 4.8 0.3 + - - -
37B ALA* 3.9 1.6 - - - +
64B THR* 3.5 27.3 - - - +
75B GLY* 3.2 4.0 - - - -
76B GLY 2.9 27.8 + - - +
854B NA 4.4 4.5 - - - -
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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
------------------------------------------------------------
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