Contacts of the strand formed by residues 24 - 32 (chain B) in PDB entry 3N4E
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 THR 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B SER* 4.4 12.6 + - - +
13B VAL 3.1 10.5 - - - -
14B ALA* 4.0 17.3 - - + +
15B MSE 4.5 1.3 - - - +
23B PRO* 1.3 82.2 - - + +
25B SER* 1.3 66.2 + - - +
44B PRO* 3.5 18.2 - - - +
47B GLY* 3.8 22.2 + - - -
49B ILE* 5.7 0.7 - - - +
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Residues in contact with SER 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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11B LEU 3.7 0.6 - - - +
12B SER* 3.5 6.2 + - - -
13B VAL 2.7 31.1 + - - -
15B MSE 3.4 23.2 - - - +
24B THR* 1.3 74.5 + - - +
26B ALA* 1.3 62.1 + - - +
27B PHE* 3.4 31.2 - - - -
41B GLU* 4.1 6.5 + - - -
44B PRO* 4.1 5.9 - - - +
47B GLY 4.3 3.2 - - - +
301B GLN* 4.0 15.6 + - - -
331B ARG* 5.1 3.3 + - - -
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Residues in contact with ALA 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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11B LEU 3.4 4.9 - - - -
25B SER* 1.3 76.1 - - - +
27B PHE* 1.3 63.1 + - - +
41B GLU* 3.4 6.9 + - - +
42B ALA* 3.0 42.1 + - + +
44B PRO* 4.3 3.8 - - + +
47B GLY 3.7 17.0 - - - +
48B GLY* 4.0 8.7 - - - +
52B LEU* 3.7 26.5 - - + -
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Residues in contact with PHE 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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11B LEU* 2.8 39.3 + - + +
13B VAL* 3.9 25.1 - - + -
15B MSE 4.0 16.2 - - + -
25B SER* 3.4 28.9 - - - -
26B ALA* 1.3 74.4 - - - +
28B VAL* 1.3 64.6 + - - +
29B ARG 4.2 0.2 - - - -
39B TRP* 4.3 20.4 - + + -
40B GLY 3.2 15.7 - - - +
41B GLU* 3.4 33.0 - - + -
52B LEU* 3.5 7.3 - - - +
304B VAL* 3.9 10.3 - - + -
335B VAL* 5.1 1.6 - - + -
336B PHE* 3.5 36.1 - + - -
364B LEU* 5.1 4.0 - - + -
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Residues in contact with VAL 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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8B VAL* 4.1 13.0 - - + -
9B GLU 3.2 9.4 - - - +
26B ALA 5.7 0.2 - - - +
27B PHE* 1.3 79.6 - - - +
29B ARG* 1.3 61.4 + - - +
30B ILE* 3.9 26.7 - - + -
38B GLY 3.5 1.0 - - - +
39B TRP* 3.4 7.2 - - - -
40B GLY 2.7 34.9 + - - +
42B ALA* 5.8 0.4 - - + -
52B LEU* 4.6 6.5 - - + -
55B VAL* 3.9 27.8 - - + -
97B ALA* 3.8 29.8 - - + +
98B CYS* 4.2 10.3 - - - -
101B ALA* 3.9 3.4 - - + +
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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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7B LYS 3.8 1.0 - - - +
8B VAL* 3.7 1.0 - - - -
9B GLU* 2.7 76.1 + - + +
11B LEU* 4.2 20.4 - - + +
27B PHE 4.2 0.4 - - - -
28B VAL* 1.3 70.8 - - - +
30B ILE* 1.3 64.8 + - - +
31B THR* 4.0 6.8 + - - +
37B VAL* 3.7 30.1 - - + -
38B GLY 3.4 3.8 - - - -
39B TRP* 3.8 33.3 - - + -
361B GLU* 3.4 21.8 + - - -
364B LEU* 3.9 13.9 - - - +
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Residues in contact with ILE 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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5B ILE* 3.5 24.7 - - + -
7B LYS 3.3 10.1 - - - +
8B VAL* 4.1 15.0 - - + -
28B VAL* 3.9 14.4 - - + -
29B ARG* 1.3 79.7 - - - +
31B THR* 1.3 63.4 + - - +
37B VAL* 3.4 1.7 - - - -
38B GLY 2.8 40.1 + - - +
63B LEU* 4.6 7.6 - - + -
98B CYS* 4.0 15.5 - - + +
101B ALA* 3.5 24.9 - - + -
102B LEU* 4.0 16.8 - - + -
105B LEU* 3.6 24.0 - - + +
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Residues in contact with THR 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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5B ILE* 3.9 1.0 - - - -
6B ALA* 2.9 23.7 + - + -
7B LYS* 2.9 36.7 + - + +
9B GLU* 3.9 16.8 + - - -
29B ARG* 4.3 3.6 - - - +
30B ILE* 1.3 74.8 - - - +
32B ALA* 1.3 73.0 + - - +
35B GLY* 4.1 15.0 - - - +
36B THR 3.4 11.2 - - - +
37B VAL* 4.0 13.1 - - + +
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Residues in contact with ALA 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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3B LEU* 3.6 23.8 - - + -
4B LYS 3.2 14.1 - - - +
5B ILE* 4.3 1.8 - - - +
6B ALA* 3.8 4.8 - - - +
30B ILE 4.0 1.4 + - - -
31B THR* 1.3 82.7 - - - +
33B GLU* 1.3 65.3 + - - +
34B ASP* 3.1 19.3 - - - +
35B GLY* 3.0 11.4 + - - -
36B THR* 3.0 13.8 + - - +
68B VAL* 4.7 0.7 - - + -
105B LEU* 4.2 11.9 - - + +
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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