Contacts of the strand formed by residues 24 - 32 (chain B) in PDB entry 4M75
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 GLU 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 3.9 14.8 - - + +
17B VAL 3.8 3.6 - - - -
18B GLU* 3.8 20.1 - - - +
22B ASP 3.5 12.7 - - - +
23B ILE* 1.3 82.4 - - - +
25B ILE* 1.3 63.3 + - - +
45B SER* 3.1 20.3 + - - -
46B THR* 3.1 43.4 + - + +
71B TYR* 4.2 14.9 + - - -
61C ARG* 4.8 5.0 + - - -
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Residues in contact with ILE 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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111A MSE 4.3 13.9 - - + -
15B VAL 3.8 0.9 - - - +
16B VAL* 3.2 2.9 - - - +
17B VAL* 2.8 42.6 + - + +
19B LEU* 4.8 10.3 - - + -
23B ILE* 4.3 11.9 - - + -
24B GLU* 1.3 80.8 - - - +
26B LYS* 1.3 74.2 + - - +
40B LEU* 5.0 6.9 - - + +
43B ILE* 4.1 17.0 - - + -
44B SER 4.2 3.1 - - - +
45B SER* 4.3 6.7 - - - +
54B LEU* 3.9 21.8 - - + -
60B ILE* 3.9 33.4 - - + -
62B ILE* 4.9 4.9 - - + -
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Residues in contact with LYS 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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14B GLU* 4.8 9.0 - - + +
15B VAL 3.3 5.6 - - - +
16B VAL* 3.4 31.9 - - + -
24B GLU 5.2 1.3 - - - +
25B ILE* 1.3 79.9 - - - +
27B GLY* 1.3 57.7 + - - +
40B LEU* 5.6 0.2 - - - -
42B ASN 3.3 4.7 - - - +
43B ILE* 3.4 3.1 - - - -
44B SER* 3.1 54.6 + - - +
45B SER 5.5 0.4 - - - -
46B THR* 5.2 13.0 - - + -
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Residues in contact with GLY 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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14B GLU* 3.6 9.3 + - - -
15B VAL 3.1 28.9 + - - +
25B ILE 4.3 0.4 + - - -
26B LYS* 1.3 75.6 - - - +
28B THR* 1.3 64.5 + - - -
29B LEU 3.8 0.2 + - - -
40B LEU* 3.5 19.7 - - - +
42B ASN 3.8 17.5 - - - -
43B ILE* 4.6 1.6 - - - -
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Residues in contact with THR 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 ASP* 3.6 32.8 - - - +
13B GLN 3.5 10.1 - - - +
14B GLU* 4.0 9.9 + - - +
27B GLY* 1.3 75.0 - - - -
29B LEU* 1.3 65.0 + - - +
30B GLN 3.6 0.5 + - - -
40B LEU* 3.3 3.8 - - - -
41B ASP* 2.9 35.7 + - - +
42B ASN* 3.7 21.3 - - - +
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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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7B PHE* 4.0 20.4 - - + +
10B LEU* 3.6 36.3 - - + +
11B VAL* 3.5 13.8 - - + -
12B ASP* 2.5 34.3 + - - +
13B GLN 3.0 12.6 + - - +
15B VAL* 4.4 9.4 - - + -
28B THR* 1.3 73.2 - - - +
30B GLN* 1.3 59.9 + - - +
31B SER 4.0 9.9 - - - +
32B VAL* 4.9 2.2 - - + -
38B LEU* 3.8 27.4 - - + -
39B LYS 3.7 13.0 - - - +
40B LEU* 3.6 18.5 - - + +
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Residues in contact with GLN 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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38A TYR* 5.0 15.7 - - + +
40A PHE* 4.3 7.8 - - - -
11B VAL* 4.2 12.3 - - - +
12B ASP* 5.4 2.2 - - - +
28B THR 4.4 5.4 - - - +
29B LEU* 1.3 74.3 - - - +
31B SER* 1.3 68.4 + - - +
39B LYS* 3.1 25.0 + - + +
40B LEU 3.9 10.1 + - - -
41B ASP* 3.3 36.2 + - + +
58B ARG* 5.8 1.8 + - - -
59B ASN* 4.3 12.0 + - - -
-1N GLY 5.8 0.2 - - - +
0N SER* 6.1 0.7 - - - -
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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
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38A TYR* 6.3 0.2 - - - -
39A ASN 4.3 5.2 + - - -
40A PHE* 3.7 22.3 - - - -
41A THR 4.5 6.9 + - - -
45A ALA* 4.6 9.8 + - - +
11B VAL* 4.2 1.5 - - - +
29B LEU* 3.8 7.4 - - - +
30B GLN* 1.3 85.7 - - - +
32B VAL* 1.3 77.9 + - - +
38B LEU* 3.8 0.3 - - - -
39B LYS* 3.0 41.7 + - - +
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Residues in contact with VAL 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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40A PHE* 3.1 34.2 - - + +
41A THR 3.9 0.6 + - - -
4B PHE* 4.0 8.1 - - + +
7B PHE* 3.7 39.7 - - + -
8B LYS* 4.2 23.3 - - + +
11B VAL* 4.8 2.7 - - + -
29B LEU* 4.9 2.7 - - + -
31B SER* 1.3 79.3 + - - +
33B ASP* 1.3 62.6 - - - +
36B LEU* 4.7 7.6 - - + -
37B ASN 3.4 10.5 - - - +
38B LEU* 3.5 33.0 - - + -
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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