Contacts of the strand formed by residues 36 - 51 (chain B) in PDB entry 4COF
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 VAL 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 3.7 11.5 - - - +
29B PRO* 4.0 18.8 - - + +
30B ASP* 5.7 2.0 - - + -
34B PRO 3.7 1.2 + - - -
35B PRO* 1.3 70.6 - - - +
37B CYS* 1.3 60.9 + - - +
38B VAL* 3.7 4.1 + - + -
67B TRP* 3.8 36.3 - - + -
68B ARG 4.1 12.8 - - - +
92B TRP* 3.9 16.8 - - + -
163B ASP 2.9 19.7 + - - +
164B ILE* 3.5 17.0 - - + +
165B GLU 2.9 24.1 + - - +
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Residues in contact with CYS 37 (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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35B PRO* 3.7 8.3 + - - -
36B VAL* 1.3 74.4 - - - +
38B VAL* 1.3 62.8 + - - +
39B GLY 3.8 0.3 + - - -
66B TYR 3.4 10.2 - - - +
67B TRP* 3.8 10.4 - - - +
68B ARG 4.9 0.7 + - - -
165B GLU* 3.3 25.6 - - - +
167B TYR* 3.8 21.0 + - + -
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.2 8.1 - - + +
37B CYS* 1.3 74.6 - - - +
39B GLY* 1.3 61.4 + - - +
40B MET* 3.7 25.0 + - + +
65B GLN* 3.9 15.5 - - + -
66B TYR 3.3 9.9 - - - +
67B TRP* 4.2 10.5 - - + -
92B TRP* 5.1 0.2 - - + -
94B PRO* 3.7 34.3 - - + -
164B ILE* 3.9 28.3 - - + -
165B GLU 2.7 10.4 + - - +
166B PHE* 3.4 5.4 - - + -
167B TYR* 3.0 27.5 + - - +
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Residues in contact with GLY 39 (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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38B VAL* 1.3 69.8 - - - +
40B MET* 1.3 61.7 + - - -
65B GLN* 3.4 2.9 - - - -
66B TYR* 2.7 50.9 + - - -
167B TYR* 3.4 33.0 - - - -
169B ARG* 4.0 7.2 - - - -
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Residues in contact with MET 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.7 16.4 - - + +
39B GLY* 1.3 73.7 - - - -
41B ASN* 1.3 60.8 + - - +
63B PHE* 3.5 32.5 - - + -
64B GLN 3.4 6.3 - - - +
65B GLN* 3.6 21.5 - - - +
96B THR* 3.7 1.6 - - - +
154B ILE* 3.9 16.2 - - + -
166B PHE* 3.5 40.8 - - + -
167B TYR 2.8 6.5 + - - +
168B TRP* 3.6 17.3 - - + -
169B ARG* 2.8 29.2 + - - +
174B ALA* 4.1 0.5 - - - +
208B LEU* 3.4 26.7 - - + -
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Residues in contact with ASN 41 (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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40B MET* 1.3 73.4 - - - +
42B ILE* 1.4 69.4 + - - +
43B ASP* 5.8 1.0 - - - +
62B TYR 3.7 1.0 - - - +
63B PHE* 3.9 0.7 - - - -
64B GLN* 2.8 42.1 + - + +
66B TYR* 3.8 21.7 + - + -
168B TRP* 5.2 0.2 - - - -
169B ARG* 3.1 45.0 + - - +
173B LYS 5.6 0.4 + - - -
174B ALA* 3.2 19.3 + - - +
176B THR* 5.4 3.1 + - - +
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Residues in contact with ILE 42 (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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41B ASN* 1.4 84.1 + - - +
43B ASP* 1.3 60.5 + - - +
44B ILE* 4.1 14.8 - - + -
61B MET* 3.7 32.8 - - + -
62B TYR 3.4 4.3 - - - +
63B PHE* 3.8 20.9 - - + -
152B LEU* 4.6 8.3 - - + -
154B ILE* 3.9 16.6 - - + -
168B TRP* 3.7 31.9 - - + -
174B ALA 3.2 9.7 + - - +
175B VAL* 3.1 16.1 - - + +
176B THR* 2.9 25.7 + - - +
210B LEU* 4.3 10.3 - - + -
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Residues in contact with ASP 43 (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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41B ASN* 5.8 1.6 - - - +
42B ILE* 1.3 72.2 - - - +
44B ILE* 1.3 68.6 + - - +
45B ALA* 3.4 2.1 + - - -
61B MET* 3.2 4.0 - - - +
62B TYR* 2.9 62.3 + - + +
176B THR* 2.5 31.8 + - - +
177B GLY* 4.2 2.3 + - - -
180B ARG* 5.4 3.3 + - - -
200C PHE* 6.6 0.2 - - - -
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Residues in contact with ILE 44 (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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42B ILE* 4.1 13.9 - - + -
43B ASP* 1.3 76.1 - - - +
45B ALA* 1.3 61.2 + - - +
46B SER 3.6 9.0 - - - +
47B ILE* 4.5 1.6 - - + -
59B LEU* 3.7 25.4 - - + -
60B THR 4.0 3.4 - - - +
61B MET* 4.3 1.8 - - + -
175B VAL* 3.8 12.3 - - + -
176B THR 2.7 14.5 + - - +
177B GLY* 3.6 21.0 - - - +
178B VAL* 3.8 16.8 - - + -
180B ARG* 5.1 3.3 - - - +
181B ILE* 3.5 27.0 - - + +
210B LEU* 4.0 4.5 - - + -
212B PHE* 3.6 35.4 - - + -
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Residues in contact with ALA 45 (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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43B ASP* 3.4 8.0 + - - -
44B ILE* 1.3 73.2 - - - +
46B SER* 1.4 67.0 + - - +
60B THR* 2.9 26.7 + - + +
61B MET 4.4 1.1 - - - +
62B TYR* 4.1 22.9 - - + -
129B ARG* 5.5 4.5 - - - +
180B ARG* 5.8 1.4 - - - +
181B ILE* 4.7 2.6 - - - +
99C LEU 5.6 3.8 - - - +
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Residues in contact with SER 46 (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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44B ILE* 3.4 5.2 - - - +
45B ALA* 1.4 81.7 - - - +
47B ILE* 1.4 66.1 + - - +
48B ASP* 3.1 27.8 + - - +
59B LEU* 3.4 4.0 - - - -
60B THR* 3.0 37.5 + - - +
181B ILE* 3.8 10.5 - - - -
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Residues in contact with ILE 47 (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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44B ILE* 4.8 0.7 - - + -
46B SER* 1.4 75.4 - - - +
48B ASP* 1.3 61.0 + - - +
49B MET 3.9 13.2 - - - +
50B VAL* 4.0 7.4 - - + -
57B TYR* 4.6 9.9 - - + -
58B THR 3.5 13.2 - - - +
59B LEU* 3.8 16.2 - - + -
181B ILE* 3.8 23.7 - - + +
182B GLU 5.0 5.1 + - - +
183B LEU* 3.4 38.3 - - + +
188B ILE* 3.9 26.5 - - + -
212B PHE* 4.2 28.5 - - + -
214B LEU* 5.5 1.8 - - + -
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Residues in contact with ASP 48 (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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46B SER* 3.1 22.7 + - - -
47B ILE* 1.3 70.9 - - - +
49B MET* 1.4 64.4 + - + +
58B THR* 3.1 20.1 + - + +
59B LEU 3.7 4.9 + - - -
60B THR* 2.8 33.9 + - - -
131B THR* 5.5 0.9 - - - -
183B LEU* 5.1 1.1 - - - +
102C LYS* 4.0 35.1 + - - +
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Residues in contact with MET 49 (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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47B ILE* 3.2 4.4 - - - +
48B ASP* 1.4 82.3 - - + +
50B VAL* 1.4 72.9 + - - +
51B SER* 4.4 11.4 - - - +
56B ASP* 5.4 2.2 - - - +
57B TYR* 3.3 7.0 - - - +
58B THR* 2.9 46.1 + - - +
183B LEU* 4.9 4.5 - - - -
54C ASN* 4.5 17.3 - - + +
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Residues in contact with VAL 50 (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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47B ILE* 4.0 15.5 - - + -
49B MET* 1.4 80.3 - - - +
51B SER* 1.3 60.7 + - - +
52B GLU* 4.0 11.6 - - - +
56B ASP 3.8 4.5 - - - +
57B TYR* 4.0 12.3 - - + -
138B MET* 3.8 24.7 - - + -
183B LEU* 4.2 16.2 - - + +
186B PHE* 3.7 33.6 - - + -
214B LEU* 4.2 21.3 - - + -
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Residues in contact with SER 51 (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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49B MET* 4.3 11.8 - - - +
50B VAL* 1.3 71.7 - - - +
52B GLU* 1.3 59.8 + - - +
53B VAL* 3.5 5.9 + - - +
54B ASN* 2.9 34.4 + - - -
55B MET* 3.1 5.0 - - - -
56B ASP* 2.8 50.8 + - - +
138B MET* 3.9 5.3 - - - +
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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