Contacts of the strand formed by residues 44 - 53 (chain F) in PDB entry 6CP3
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 GLY 44 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40F LYS* 3.7 7.7 - - - +
41F THR* 2.9 33.6 + - - +
42F PRO 3.3 1.2 - - - -
43F GLN* 1.3 81.0 - - - +
45F LYS* 1.3 61.2 + - - +
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Residues in contact with LYS 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLU* 3.4 24.1 + - + +
39F ILE 3.4 12.6 - - - +
40F LYS* 4.5 15.3 - - + +
41F THR* 3.7 5.2 + - - -
43F GLN 5.5 0.5 - - - +
44F GLY* 1.3 74.8 - - - +
46F LEU* 1.3 64.4 + - - +
47F VAL* 3.6 24.3 - - + +
65F ASP* 6.0 0.9 - - - +
99F ILE* 4.0 15.7 - - - +
101F GLU* 3.2 29.2 + - - +
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Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLU* 3.3 3.7 - - - +
39F ILE* 2.9 37.5 + - + +
41F THR* 3.7 22.4 - - + -
45F LYS* 1.3 80.0 - - - +
47F VAL* 1.3 66.7 + - - +
48F LEU* 3.7 28.6 + - + +
63F ALA* 5.3 0.2 - - + -
65F ASP* 4.6 20.6 - - + +
66F GLY 3.3 30.3 - - - +
67F THR* 4.3 14.6 - - + -
70F LEU* 4.9 11.4 - - + -
99F ILE* 5.8 1.6 - - - -
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Residues in contact with VAL 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F ALA* 4.4 13.7 - - + -
37F LEU 3.5 11.2 - - - +
38F GLU* 4.6 9.6 - - + +
45F LYS* 3.6 27.1 - - - +
46F LEU* 1.3 79.1 - - - +
48F LEU* 1.3 72.3 + - - +
64F MET* 3.0 38.8 + - + +
65F ASP* 4.3 3.4 + - - +
83F ILE* 4.4 10.3 - - + -
99F ILE* 3.8 35.6 - - + +
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F VAL* 5.7 0.2 - - + -
21F VAL* 3.7 32.8 - - + -
23F VAL* 4.6 13.7 - - + -
36F ALA* 3.3 6.6 - - - +
37F LEU* 2.9 45.7 + - + +
39F ILE* 3.7 28.7 - - + -
46F LEU* 3.7 22.9 - - + +
47F VAL* 1.3 87.2 - - - +
49F GLU* 1.3 62.3 + - - +
61F THR* 3.9 14.1 - - - +
62F ILE 3.5 2.2 - - - -
63F ALA* 3.7 16.2 - - + -
64F MET* 5.0 1.3 - - - -
67F THR* 5.0 0.2 - - + -
70F LEU* 6.1 0.2 - - + -
76F VAL* 4.9 0.2 - - + -
83F ILE* 5.2 0.2 - - - +
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Residues in contact with GLU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 3.4 20.7 - - - +
35F ASN 3.5 9.0 - - - +
48F LEU* 1.3 76.0 - - - +
50F VAL* 1.3 65.5 + - - +
51F ALA* 3.3 0.9 + - - -
61F THR* 3.2 3.9 - - - -
62F ILE* 2.9 34.7 + - + +
64F MET* 3.4 21.1 - - + +
83F ILE* 4.3 14.2 - - + +
118F HIS* 2.4 35.7 + - - -
231F ARG* 2.4 40.1 + - - +
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F PRO* 4.3 9.0 - - + +
32F ALA 3.6 24.2 - - - +
33F ILE* 4.0 14.9 - - + +
34F LEU* 3.0 25.1 + - - +
35F ASN 3.0 18.0 + - - +
37F LEU* 3.9 24.2 - - + -
49F GLU* 1.3 72.5 - - - +
51F ALA* 1.3 63.1 - - - +
52F GLN 4.6 1.3 - - - +
53F HIS* 4.6 0.7 - - + +
59F VAL* 4.0 29.6 - - + -
61F THR* 3.6 19.5 - - + -
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Residues in contact with ALA 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLY* 4.6 5.4 - - - -
38C ASP* 5.3 2.8 + - - +
81C ASP* 4.7 0.5 - - - +
33F ILE* 3.3 23.8 - - - +
34F LEU* 5.8 2.0 - - - -
49F GLU 3.3 1.4 + - - -
50F VAL* 1.3 72.9 - - - +
52F GLN* 1.3 66.4 + - + +
60F ARG 3.1 15.1 + - - +
62F ILE* 4.0 32.1 - - + -
231F ARG* 5.9 1.6 - - - +
272F LEU* 4.5 12.1 - - + -
274F ARG* 6.0 2.0 - - - +
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Residues in contact with GLN 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLY* 4.1 17.7 + - - +
38C ASP* 3.5 23.1 - - - +
33F ILE* 4.2 4.7 - - - -
50F VAL* 4.0 0.6 - - - -
51F ALA* 1.3 82.2 - - + +
53F HIS* 1.3 65.1 + - - +
54F LEU* 4.2 13.8 - - + +
59F VAL* 3.7 2.2 - - - -
60F ARG* 2.9 59.6 + - + +
272F LEU* 3.0 33.3 + - + +
274F ARG* 6.5 0.2 - - - -
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Residues in contact with HIS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ALA* 3.3 25.6 - - - +
36C VAL* 3.8 29.6 + - + +
84C VAL 3.9 8.6 + - - -
85C LYS* 4.1 5.3 - - - -
86C GLU* 4.4 20.9 - - + +
30F LEU* 3.9 18.3 - - + +
31F PRO 3.2 27.4 + - - -
32F ALA* 4.3 1.4 - - - -
33F ILE* 3.5 36.8 + - + +
50F VAL* 4.6 0.7 - - + -
52F GLN* 1.3 75.8 - - - +
54F LEU* 1.3 59.1 + - - +
55F GLY 3.2 8.3 - - - +
58F THR 3.7 4.7 - - - +
59F VAL* 3.3 21.6 - - + +
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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