Contacts of the strand formed by residues 25 - 36 (chain E) in PDB entry 3OF6
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 GLN 25 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E MET* 3.1 41.2 - - + +
19E LEU 3.4 11.9 - - - +
20E LEU* 4.0 6.2 - - - +
23E GLY 4.2 1.2 + - - -
24E LYS* 1.3 75.3 - - - +
26E GLN* 1.3 70.0 + - - +
79E PRO* 4.5 0.3 - - - +
80E SER* 3.0 44.4 + - - +
81E GLU* 4.0 6.4 + - - +
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Residues in contact with GLN 26 (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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17E ILE 3.4 5.0 - - - +
18E MET* 3.7 3.3 - - - -
19E LEU* 2.7 45.6 + - + +
21E VAL* 3.6 33.9 - - + +
24E LYS* 4.5 2.1 - - - +
25E GLN* 1.3 82.4 - - - +
27E MET* 1.3 59.0 + - - +
28E VAL* 3.8 10.1 + - + +
77E SER* 2.7 29.6 + - - +
78E LEU* 3.6 21.1 - - - +
79E PRO* 3.8 13.7 - - - +
80E SER* 4.3 2.9 - - - -
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Residues in contact with MET 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E PRO* 3.4 41.7 - - + -
17E ILE 3.8 4.5 - - - +
18E MET* 4.6 14.8 - - + -
26E GLN* 1.3 71.0 - - - +
28E VAL* 1.3 64.0 + - - +
29E VAL* 3.8 25.8 - - + -
76E LEU 3.9 0.7 - - - +
77E SER* 3.6 0.5 - - - -
78E LEU* 2.7 67.6 + - + +
79E PRO 4.4 1.1 - - - +
80E SER* 4.1 16.2 - - - +
83E LEU* 5.7 3.8 - - + -
89E LEU* 5.1 7.4 - - + -
109E LEU* 4.3 21.8 - - + -
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Residues in contact with VAL 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE* 3.2 26.3 - - + -
149B LEU* 5.2 1.3 - - + -
17E ILE* 2.9 47.1 + - + -
19E LEU* 4.7 12.6 - - + -
26E GLN* 4.1 13.2 - - + +
27E MET* 1.3 81.2 - - - +
29E VAL* 1.3 66.6 + - - +
75E HIS* 4.4 17.9 - - + -
76E LEU 3.4 8.1 - - - +
77E SER* 3.8 19.3 - - - +
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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
----------------------------------------------------------
131B PHE* 4.1 4.9 - - - -
13E LEU* 4.4 17.5 - - + -
14E ALA 3.1 24.7 - - - +
16E PRO* 4.4 10.1 - - + -
27E MET* 3.8 16.1 - - + +
28E VAL* 1.3 75.0 - - - +
30E VAL* 1.3 73.9 + - - +
47E PHE* 5.0 2.1 - - + -
75E HIS* 3.5 2.9 - - - +
76E LEU* 2.8 45.3 + - + +
89E LEU* 3.8 28.5 - - + -
107E MET* 5.0 3.6 - - - -
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Residues in contact with VAL 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE* 3.5 37.4 - - + -
147B VAL* 4.2 14.6 - - + -
149B LEU* 4.5 2.0 - - + -
12E SER 4.0 0.2 - - - +
13E LEU* 3.8 3.6 - - - -
14E ALA* 3.0 41.8 + - + +
29E VAL* 1.3 80.9 - - - +
31E CYS* 1.3 63.4 + - - +
32E LEU* 6.2 0.9 - - + -
47E PHE* 5.2 0.7 - - - -
73E LEU* 3.4 33.7 - - + -
74E ALA 3.5 14.1 - - - +
75E HIS* 4.3 9.4 - - + -
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Residues in contact with CYS 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E PRO* 4.2 6.1 - - - -
12E SER 3.7 20.4 - - - -
13E LEU* 3.7 10.8 - - + -
30E VAL* 1.3 74.7 - - - +
32E LEU* 1.3 64.6 + - - +
33E VAL 4.2 0.2 - - - -
45E ILE* 3.9 12.7 - - + +
47E PHE* 3.7 14.1 - - + -
73E LEU* 3.3 16.9 - - - +
74E ALA 3.0 18.7 + - - +
91E CYS* 2.0 46.7 - - - -
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Residues in contact with LEU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU* 4.8 7.0 - - - +
145B THR* 3.8 33.4 - - + +
147B VAL* 4.5 13.2 - - + -
196B ARG* 4.3 11.2 - - - -
10E PHE 3.6 1.9 - - - +
11E PRO* 3.3 2.0 - - - +
12E SER* 3.0 41.2 + - - +
14E ALA* 6.5 1.3 - - + -
30E VAL* 4.2 1.1 - - + -
31E CYS* 1.3 73.6 - - - +
33E VAL* 1.3 60.1 + - - +
34E LEU* 3.7 20.5 + - + +
71E THR* 4.0 20.6 - - - -
72E ASN 3.5 17.9 - - - +
73E LEU* 3.6 17.9 - - + -
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Residues in contact with VAL 33 (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 PRO* 4.0 7.2 - - + -
10E PHE 3.5 15.9 - - - +
11E PRO* 3.7 10.5 - - + -
31E CYS* 4.2 1.0 - - - -
32E LEU* 1.3 72.3 - - - +
34E LEU* 1.3 73.7 + - - +
36E VAL* 3.6 12.3 - - + +
43E SER* 4.2 2.5 - - - +
45E ILE* 3.7 15.2 - - + +
71E THR* 3.4 9.4 - - - -
72E ASN* 3.2 50.5 + - + +
93E THR* 3.4 25.4 - - + +
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Residues in contact with LEU 34 (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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137B GLU* 3.9 32.3 - - + +
141B THR* 4.9 7.6 - - + -
145B THR* 5.5 1.6 - - + +
198B ARG* 4.4 23.3 - - - +
9E PRO* 3.0 4.0 - - - +
10E PHE* 2.8 47.4 + - + +
12E SER* 5.3 1.8 - - - +
32E LEU* 3.7 32.3 - - + +
33E VAL* 1.3 75.7 - - - +
35E ASP* 1.3 77.3 + - - +
36E VAL 2.9 7.2 + - - -
69E THR* 6.4 0.2 - - + -
71E THR* 3.5 25.8 - - + -
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Residues in contact with ASP 35 (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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140B HIS* 4.7 10.7 + - - -
7E GLY 3.8 19.5 + - - +
8E THR* 3.0 36.9 + - - +
9E PRO* 3.4 13.7 - - - +
10E PHE* 4.4 7.9 - - - +
34E LEU* 1.3 79.6 - - - +
36E VAL* 1.3 63.7 + - - +
37E ALA 3.3 2.9 + - - -
69E THR* 4.0 17.9 + - - +
70E TRP 3.9 3.2 + - - -
71E THR* 5.0 1.0 - - - +
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Residues in contact with VAL 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLY 5.9 0.2 - - - -
9E PRO* 4.5 4.9 - - - -
33E VAL* 3.6 39.9 - - + +
34E LEU 2.9 6.9 + - - +
35E ASP* 1.3 74.6 - - - +
37E ALA* 1.3 77.6 + - - +
38E PRO* 3.4 2.6 - - - +
39E PRO* 5.3 0.4 - - + -
41E LEU 4.5 9.0 - - - +
43E SER* 3.5 26.7 - - - +
62E PRO* 5.2 9.4 - - + -
69E THR* 3.8 3.1 + - - -
70E TRP* 3.2 42.9 + - + +
72E ASN* 4.1 7.0 - - + +
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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