Contacts of the strand formed by residues 23 - 32 (chain B) in PDB entry 4MD4
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 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* 3.7 0.2 - - - -
18B PHE* 2.9 59.6 + - + +
19B ASN* 5.6 2.2 - - + -
20B GLY 4.5 0.3 - - - +
22B GLU* 1.3 85.5 - - + +
24B VAL* 1.3 67.0 + - - +
80B ARG* 4.5 0.2 - - - +
500B NAG 5.4 15.5 - - + +
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Residues in contact with VAL 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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16B HIS 3.3 9.4 - - - +
17B PHE* 3.7 23.6 - - + -
18B PHE* 4.9 0.9 - - - -
21B THR* 3.7 9.9 - - - +
23B ARG* 1.3 81.3 - - - +
25B ARG* 1.3 64.9 + - - +
42B SER* 4.4 1.4 + - - -
75B VAL* 3.5 21.0 - - + +
79B CYS* 3.6 32.8 - - + -
80B ARG* 3.5 41.0 + - + +
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Residues in contact with ARG 25 (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 GLU 3.7 0.7 - - - +
15B CYS* 3.6 1.9 - - - -
16B HIS* 2.8 46.4 + - + +
18B PHE* 4.2 22.1 - - + -
24B VAL* 1.3 76.3 - - - +
26B PHE* 1.3 62.2 + - - +
27B LEU* 3.6 19.4 - - + +
39B ARG* 4.9 6.5 - - - +
41B ASP* 2.4 37.1 + - - +
42B SER* 3.5 11.7 - - - +
43B ASP* 3.0 31.7 + - - +
75B VAL* 4.2 1.3 - - - -
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Residues in contact with PHE 26 (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 HIS* 4.2 5.2 - - + -
14B GLU 3.2 16.2 - - - -
25B ARG* 1.3 74.3 - - - +
27B LEU* 1.3 74.5 + - - +
28B ASP* 3.4 31.6 - - + -
40B PHE* 3.8 22.7 - + - -
41B ASP* 3.7 0.2 - - - -
42B SER* 2.9 35.3 + - - +
71B LYS* 3.8 17.0 - - + -
74B ALA* 3.7 17.7 - - + -
75B VAL* 3.7 20.6 - - + +
78B TYR* 3.8 24.9 - + - -
79B CYS* 3.8 18.8 - - - -
7C CIR 3.5 16.4 - - - -
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Residues in contact with LEU 27 (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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12B LYS 3.5 1.6 - - - +
13B HIS* 3.4 3.1 - - - -
14B GLU* 2.8 58.5 + - + +
16B HIS* 3.8 20.6 - - + +
25B ARG* 3.6 17.7 - - + +
26B PHE* 1.3 91.0 - - - +
28B ASP* 1.3 58.8 + - - +
29B ARG* 3.8 25.4 - - + +
39B ARG* 5.0 16.6 - - - +
40B PHE 3.2 5.2 - - - +
41B ASP* 3.5 31.4 - - + +
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Residues in contact with ASP 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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12B LYS 4.0 1.1 - - - -
13B HIS* 2.7 30.6 + - - -
26B PHE* 3.4 17.1 - - + -
27B LEU* 1.3 70.5 - - - +
29B ARG* 1.3 58.4 + - - +
30B TYR* 2.7 30.2 + - + -
39B ARG* 3.1 6.2 - - - -
40B PHE* 2.9 47.1 + - + -
47B TYR* 2.7 22.5 + - - +
71B LYS* 3.3 15.2 + - - -
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Residues in contact with ARG 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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141A GLU* 5.3 1.0 + - - +
143A HIS* 3.5 31.1 + - - -
11B VAL* 3.3 8.6 - - - +
12B LYS 2.9 39.2 + - - +
14B GLU* 2.8 49.3 + - - -
27B LEU* 3.8 23.2 - - + +
28B ASP* 1.3 75.5 - - - +
30B TYR* 1.3 63.7 + - - +
31B PHE* 3.5 20.0 - - + -
36B GLU* 2.9 41.4 + - - +
38B VAL 4.0 4.0 - - - -
39B ARG* 3.6 15.0 - - + +
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Residues in contact with TYR 30 (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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69A ASN* 4.3 5.2 - - - -
9B GLU* 4.3 3.1 - - - -
10B GLN 3.7 2.2 - - - +
11B VAL* 3.7 31.9 - - + -
13B HIS* 4.3 0.7 - - - -
28B ASP* 2.7 47.3 + - - -
29B ARG* 1.3 75.2 - - - +
31B PHE* 1.3 61.3 + - - +
36B GLU* 3.3 5.9 - - - +
37B TYR* 2.9 52.0 + - + -
38B VAL* 3.1 21.9 + - + +
47B TYR* 4.0 10.3 - + - -
61B TRP* 4.0 16.4 - + - -
8C VAL 4.2 0.2 + - - -
9C ASN* 3.6 9.0 - - + -
10C SER* 2.8 44.2 + - - -
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Residues in contact with PHE 31 (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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143A HIS* 3.2 50.7 - + + -
9B GLU* 3.5 10.6 - - - +
10B GLN* 2.8 61.9 + - + +
12B LYS* 3.7 21.1 - - + -
29B ARG* 3.5 43.7 - - + -
30B TYR* 1.3 74.8 - - - +
32B TYR* 1.3 59.8 + - - +
33B HIS 4.2 9.9 - - - +
34B GLN 4.4 1.6 - - - -
35B GLU 3.3 7.2 - - - +
36B GLU* 3.5 32.8 - - + -
37B TYR* 3.5 6.3 - - - -
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Residues in contact with TYR 32 (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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70A LEU* 3.8 21.3 - - + -
73A MET* 3.6 18.6 - - + -
74A THR* 3.5 15.6 - - - -
77A SER* 3.0 32.0 + - - -
80A THR* 2.9 19.1 + - + -
7B PHE* 3.3 16.0 - - + -
8B LEU 3.7 9.6 - - - -
9B GLU* 4.4 2.0 - - - -
31B PHE* 1.3 72.5 - - - +
33B HIS* 1.3 93.6 + + - +
35B GLU* 2.9 35.8 + - - +
37B TYR* 3.5 16.9 - - + -
53B LEU* 4.0 23.1 - - + -
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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