Contacts of the strand formed by residues 26 - 31 (chain E) in PDB entry 1N9S
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 26 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E HIS* 1.3 71.2 - - - +
27E VAL* 1.3 55.7 + - - +
39E ARG* 5.3 9.9 + - - +
40E GLY* 3.5 17.9 - - - +
41E THR* 4.0 20.8 + - - +
54E ASN 5.5 0.2 + - - -
55E GLU* 5.0 9.9 + - - +
57E GLU* 4.6 14.3 + - - +
83E GLU* 3.7 3.7 - - - +
84E LEU* 2.7 62.0 + - + +
85E PRO 5.6 0.4 - - - +
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Residues in contact with VAL 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LEU* 4.3 25.8 - - + -
25E HIS* 3.3 18.4 - - + +
26E ARG* 1.3 77.0 - - - +
28E GLY* 1.3 61.7 + - - +
29E VAL* 4.4 4.0 - - + -
39E ARG* 3.2 3.3 - - - -
40E GLY 2.5 46.4 + - - +
42E LEU* 4.2 18.6 - - + -
51E LEU* 6.5 0.2 - - + -
53E LEU* 3.5 23.1 - - + -
81E ILE* 4.1 15.9 - - + -
82E ARG 3.3 13.2 - - - +
83E GLU* 4.7 0.2 - - - -
84E LEU* 3.3 8.7 - - - +
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Residues in contact with GLY 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E VAL* 1.3 76.0 - - - +
29E VAL* 1.3 62.7 + - - -
30E LYS 3.8 1.0 + - - -
37E GLU* 4.0 18.2 - - - -
38E TYR 3.4 5.4 - - - -
39E ARG* 4.2 6.7 - - - -
80E TYR 3.8 0.3 - - - +
81E ILE* 3.3 6.4 - - - +
82E ARG* 2.9 35.7 + - - +
84E LEU* 3.8 5.2 - - - +
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Residues in contact with VAL 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E VAL* 4.4 15.3 - - + -
28E GLY* 1.3 74.0 - - - +
30E LYS* 1.3 64.3 + - - +
31E LEU* 3.6 4.8 + - + -
37E GLU* 3.1 3.7 - - - +
38E TYR* 2.7 48.9 + - + +
51E LEU* 4.4 13.0 - - + -
53E LEU* 4.4 8.3 - - + -
73E ILE* 4.2 27.1 - - + -
78E VAL* 3.8 36.1 - - + -
80E TYR 3.8 2.7 - - - +
81E ILE* 4.5 9.0 - - + +
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Residues in contact with LYS 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLY 3.8 1.0 + - - -
29E VAL* 1.3 71.7 - - - +
31E LEU* 1.3 69.4 + - - +
35E SER* 4.1 33.3 + - - +
36E THR 3.9 3.1 - - - +
37E GLU* 4.0 23.4 + - + +
61E ALA* 6.3 0.4 - - - +
78E VAL* 3.8 2.4 - - - -
79E LEU* 2.9 39.9 + - + +
80E TYR* 2.9 62.1 + - + +
58F GLU* 5.9 2.7 - - - -
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Residues in contact with LEU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LEU* 3.8 24.7 - - + -
29E VAL* 3.6 7.6 + - + +
30E LYS* 1.3 81.6 - - - +
32E LYS* 1.3 67.0 - - - +
33E PHE* 3.2 17.3 + - + +
34E ASN 3.5 15.2 + - - +
35E SER* 5.2 0.2 - - - -
36E THR* 2.9 36.4 + - + +
38E TYR* 3.2 47.6 - - + +
73E ILE* 5.0 4.7 - - + -
77E ASN* 3.3 22.9 - - + +
78E VAL* 4.6 4.5 - - + +
79E LEU* 4.3 1.9 - - - +
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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