Contacts of the strand formed by residues 5 - 14 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 3.8 25.3 - - + +
3D LYS* 3.9 30.4 + - + -
3E LYS 5.0 0.9 - - - -
4E PRO* 1.3 74.8 - - - +
6E VAL* 1.3 58.8 + - - +
7E THR 4.0 0.4 - - - -
37E HIS* 3.1 28.8 + + + -
77E THR* 3.5 31.2 + - + +
78E PRO* 3.3 20.5 + - + +
79E PHE* 3.3 16.1 - + + -
80E LEU 2.9 25.1 + - - -
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Residues in contact with VAL 6 (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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2D PHE 5.8 0.4 + - - -
3D LYS* 5.1 1.6 - - - +
4D PRO* 3.4 35.0 - - + -
80D LEU* 4.0 13.7 - - + -
4E PRO* 3.5 14.3 + - + +
5E HIS* 1.3 75.2 - - - +
7E THR* 1.3 61.9 + - - +
37E HIS* 3.5 4.6 - - - +
38E LEU* 2.8 44.0 + - + +
44E LEU* 4.6 2.2 - - + -
80E LEU* 3.3 8.3 - - + +
82E PHE* 3.2 37.0 - - + -
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Residues in contact with THR 7 (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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5E HIS 4.0 0.4 - - - -
6E VAL* 1.3 76.6 - - - +
8E VAL* 1.3 62.3 + - - +
36E GLY 3.1 22.0 - - - +
37E HIS* 3.8 16.4 - - + +
79E PHE* 3.7 31.5 - - + -
80E LEU 2.8 10.5 + - - +
81E ARG* 3.2 15.3 - - - +
82E PHE* 3.0 30.1 + - - -
158E SO4 2.9 30.9 + - - +
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Residues in contact with VAL 8 (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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7E THR* 1.3 80.3 - - - +
9E ALA* 1.3 54.9 + - - +
35E ALA* 2.8 29.4 - - - +
36E GLY 2.7 29.8 + - - +
37E HIS 5.0 0.9 - - - -
38E LEU 5.7 1.6 - - - +
44E LEU* 3.7 40.8 - - + +
47E ALA* 3.7 16.4 - - + +
48E ALA* 3.5 33.4 - - + +
51E GLU* 4.9 2.7 - - + -
81E ARG* 5.1 0.2 - - - -
82E PHE* 3.4 7.9 - - + +
84E PHE* 4.0 11.7 - - + -
158E SO4 5.0 0.4 - - - -
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Residues in contact with ALA 9 (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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8E VAL* 1.3 76.1 - - - +
10E CYS* 1.3 58.8 + - - +
33E GLN* 4.1 3.4 - - + -
34E PRO 3.6 0.9 - - - -
35E ALA* 3.4 19.7 - - + -
81E ARG* 3.6 36.3 - - - +
82E PHE 2.8 11.5 + - - +
83E LEU* 3.4 10.8 - - + -
84E PHE* 2.7 35.7 + - - -
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Residues in contact with CYS 10 (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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9E ALA* 1.3 79.1 - - - +
11E VAL* 1.3 64.1 + - - +
12E VAL* 3.4 19.5 + - + -
33E GLN* 3.4 7.8 - - - +
34E PRO* 3.1 36.2 + - + +
48E ALA* 4.0 35.0 - - - -
49E ALA* 5.7 0.2 - - - -
52E LEU* 4.6 9.4 - - + -
62E PRO* 4.6 2.2 - - - -
84E PHE* 3.4 11.9 - - - +
86E ILE* 4.2 20.0 - - + -
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Residues in contact with VAL 11 (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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9E ALA 4.2 0.4 - - - -
10E CYS* 1.3 70.9 - - - +
12E VAL* 1.3 59.0 + - - +
13E HIS 4.2 0.2 + - - -
18E PHE* 3.8 18.4 - - + -
19E LEU 6.0 0.2 - - - -
33E GLN* 4.0 21.3 - - + +
66E ILE* 4.3 4.7 - - + -
83E LEU* 4.0 17.5 - - + -
84E PHE 2.6 14.8 + - - +
85E ALA* 3.5 0.5 - - - -
86E ILE 2.8 28.1 + - - +
126E SER* 4.2 21.5 - - - +
127E ILE* 4.9 3.6 - - + -
130E TYR* 3.2 39.6 - - + -
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Residues in contact with VAL 12 (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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10E CYS* 3.4 27.0 + - + +
11E VAL* 1.3 77.6 - - - +
13E HIS* 1.3 63.8 + - - +
18E PHE* 3.2 6.9 - - - -
19E LEU* 2.8 48.9 + - + +
34E PRO* 4.7 2.9 - - + -
52E LEU* 4.5 21.3 - - + -
58E ILE* 5.5 0.7 - - + -
86E ILE* 3.4 23.1 - - + +
88E LEU* 3.6 32.3 - - + -
106E TRP* 3.9 6.1 - - + -
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Residues in contact with HIS 13 (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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12E VAL* 1.3 76.3 - - - +
14E ALA* 1.3 60.6 + - - +
15E GLU 4.7 1.4 + - - -
16E GLY* 3.6 35.6 + - - -
17E LYS 3.1 17.6 + - - -
18E PHE* 3.3 30.4 - + + -
86E ILE 3.0 6.7 + - - +
87E GLU* 3.0 28.5 - - - +
88E LEU* 2.8 30.5 + - - +
106E TRP* 4.0 1.8 - - - -
130E TYR* 3.0 28.3 + + + +
137F PRO* 6.2 2.4 - - - +
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Residues in contact with ALA 14 (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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13E HIS* 1.3 81.0 - - - +
15E GLU* 1.3 71.1 + - - +
16E GLY 3.4 1.3 - - - -
17E LYS* 3.1 14.8 + - - +
88E LEU* 3.6 23.6 - - + +
90E GLN* 3.9 4.9 - - - -
91E ILE* 3.3 40.0 - - + +
106E TRP* 3.7 9.2 - - + -
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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