Contacts of the strand formed by residues 5 - 14 (chain J) in PDB entry 3SHD
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 HIS 5 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3J LYS 5.1 2.9 - - - -
4J PRO* 1.3 76.9 - - + +
6J VAL* 1.3 62.0 + - - +
7J THR 4.0 0.2 - - - -
37J HIS* 3.0 29.6 + + - +
77J THR* 4.3 19.8 - - + +
78J PRO* 2.9 27.9 + - + +
79J PHE* 3.4 23.0 - + + -
80J LEU* 2.9 26.7 + - - +
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Residues in contact with VAL 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J PRO* 3.7 10.4 + - + +
5J HIS* 1.3 77.6 - - - +
7J THR* 1.3 69.8 + - - +
37J HIS* 3.6 7.3 - - - -
38J LEU* 3.0 42.3 + - + +
44J LEU* 3.8 28.9 - - + -
80J LEU* 3.5 22.2 - - + -
82J PHE* 3.8 15.7 - - + -
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Residues in contact with THR 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J HIS 4.0 0.2 + - - -
6J VAL* 1.3 79.6 - - - +
8J VAL* 1.3 62.4 - - - +
36J GLY 3.3 18.2 - - - +
37J HIS* 3.5 30.1 - - + +
38J LEU 4.4 0.4 - - - +
79J PHE* 3.8 14.6 - - + -
80J LEU 2.9 8.8 + - - +
81J ARG* 3.5 15.6 - - - +
82J PHE* 2.7 37.1 + - - -
158J SO4 2.6 30.4 + - - +
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Residues in contact with VAL 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J THR* 1.3 81.9 - - - +
9J ALA* 1.3 64.5 + - - +
35J ALA* 3.2 2.9 - - - +
36J GLY 3.0 34.6 + - - +
38J LEU* 5.1 2.7 - - + +
44J LEU* 3.7 41.7 - - + +
47J ALA* 3.9 15.0 - - + +
48J ALA* 3.5 33.2 - - + +
51J GLU* 4.5 6.7 - - + -
81J ARG* 4.8 0.9 - - - -
82J PHE* 3.1 10.3 - - + +
84J PHE* 4.3 8.3 - - + -
158J SO4 4.7 0.3 + - - -
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Residues in contact with ALA 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J VAL* 1.3 80.4 - - - +
10J CYS* 1.3 69.0 + - - +
33J GLN* 4.4 2.0 - - + -
34J PRO 3.4 9.9 - - - +
35J ALA* 3.6 7.9 - - + -
48J ALA* 5.9 0.2 - - - +
81J ARG* 3.4 38.6 - - + +
82J PHE 2.8 6.8 + - - +
83J LEU* 3.8 11.0 - - + -
84J PHE* 3.0 25.6 + - - -
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Residues in contact with CYS 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ALA* 1.3 84.2 - - - +
11J VAL* 1.3 62.1 + - - +
12J VAL* 3.5 22.1 + - + -
19J LEU 5.0 0.3 - - - +
33J GLN* 3.2 20.6 - - - +
34J PRO* 3.0 20.7 + - + +
48J ALA* 3.7 34.8 - - - -
52J LEU* 4.9 7.9 - - + -
62J PRO* 4.5 0.9 - - - -
83J LEU* 4.5 0.2 - - - -
84J PHE* 3.5 13.0 - - - +
86J ILE* 3.9 22.4 - - + -
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Residues in contact with VAL 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J CYS* 1.3 70.8 - - - +
12J VAL* 1.3 60.2 + - - +
13J HIS* 4.8 0.5 - - - +
18J PHE* 3.7 25.1 - - + -
19J LEU 5.8 0.2 - - - -
33J GLN* 4.0 21.3 - - + +
66J ILE* 4.4 5.6 - - + -
83J LEU* 4.0 17.0 - - + +
84J PHE 2.8 14.0 + - - +
85J ALA* 3.5 3.3 - - - +
86J ILE 3.1 25.3 + - - +
126J SER* 4.1 21.5 - - - +
127J ILE* 4.2 3.6 - - + -
130J TYR* 3.5 33.2 - - + -
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Residues in contact with VAL 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J CYS* 3.5 28.8 + - + +
11J VAL* 1.3 73.7 - - - +
13J HIS* 1.3 61.6 + - - +
18J PHE* 3.6 5.9 - - - +
19J LEU* 3.1 46.5 + - + +
34J PRO* 4.3 8.5 - - + -
52J LEU* 4.2 26.7 - - + -
58J ILE* 5.5 0.2 - - + -
86J ILE* 3.3 15.3 - - + +
88J LEU* 3.6 34.3 - - + -
106J TRP* 4.3 1.3 - - + -
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Residues in contact with HIS 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J VAL 4.8 0.2 - - - +
12J VAL* 1.3 77.3 - - - +
14J ALA* 1.3 64.2 + - - +
15J GLU 4.7 1.0 + - - -
16J GLY* 3.8 33.9 + - - -
17J LYS 3.2 16.3 + - - -
18J PHE* 3.5 33.7 - + + -
86J ILE 3.0 6.1 + - - -
87J GLU* 2.8 41.8 + - - +
88J LEU* 2.9 26.4 + - - +
106J TRP* 4.5 1.6 - - - -
130J TYR* 3.1 19.9 + + + +
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Residues in contact with ALA 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J HIS* 1.3 84.2 - - - +
15J GLU* 1.3 72.4 + - + +
16J GLY 3.2 2.0 - - - -
17J LYS* 2.9 21.3 + - - +
88J LEU* 3.5 28.9 - - + +
90J GLN 4.3 0.9 - - - -
91J ILE* 3.5 32.8 - - + +
106J TRP* 4.2 8.4 - - + -
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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