Contacts of the strand formed by residues 11 - 17 (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 11 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F THR* 1.3 74.7 - - - +
12F LYS* 1.3 66.3 + - - +
23F VAL* 4.0 3.8 - - - -
24F HIS 3.2 14.1 - - - -
25F PHE* 3.9 11.1 - - - -
26F GLU 5.6 0.2 - - - -
75F LYS* 3.4 8.7 - - - +
76F VAL* 2.8 35.4 + - - -
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Residues in contact with LYS 12 (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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11F GLY* 1.3 78.8 - - - +
13F VAL* 1.3 63.5 + - - +
14F THR* 3.3 10.7 + - + +
23F VAL* 3.2 3.1 - - - +
24F HIS* 2.9 41.9 + - + +
26F GLU* 4.8 15.9 - - - +
73F GLY* 3.9 30.9 + - - +
74F GLU 3.6 3.6 - - - -
75F LYS* 5.8 0.4 - - - -
76F VAL* 4.0 4.3 - - - -
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Residues in contact with VAL 13 (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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12F LYS* 1.3 70.0 - - - +
14F THR* 1.3 62.1 + - - +
15F ALA 4.0 7.9 - - - +
16F VAL* 3.8 29.2 - - + -
21F VAL* 5.2 5.8 - - + -
22F ASP 3.4 9.0 - - - +
23F VAL* 4.7 3.6 - - + -
39F ILE* 3.8 17.9 - - + -
70F LEU* 4.5 11.2 - - + -
71F VAL 3.9 19.3 - - - +
72F ARG* 3.2 6.8 - - + +
73F GLY* 2.4 30.1 + - - -
74F GLU* 3.2 16.4 + - + +
76F VAL* 3.7 19.1 - - + -
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Residues in contact with THR 14 (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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70B PRO* 3.4 18.0 - - - +
12F LYS* 3.6 18.4 - - + +
13F VAL* 1.3 78.2 - - - +
15F ALA* 1.3 62.9 + - - +
22F ASP* 2.9 21.4 + - - +
24F HIS* 3.7 24.7 + - + +
58F THR* 4.8 3.5 - - - +
72F ARG* 3.6 21.0 - - - +
13Y PHE* 3.9 31.1 - - + -
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Residues in contact with ALA 15 (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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68B LEU* 3.3 17.3 - - - +
69B GLU* 4.0 0.9 - - + -
70B PRO* 3.7 15.9 - - + -
13F VAL* 3.7 2.4 - - - +
14F THR* 1.3 81.8 + - - +
16F VAL* 1.3 66.0 + - - +
17F ILE* 4.5 7.6 - - + -
20F ILE 4.6 0.7 - - - -
21F VAL* 3.3 5.2 - - - +
22F ASP* 2.8 52.8 + - + +
72F ARG* 5.1 0.4 - - - -
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Residues in contact with VAL 16 (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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51B ALA* 3.8 25.4 - - + -
66B LEU 5.8 0.9 - - - +
67B ASN* 3.5 1.6 - - - -
68B LEU* 2.6 50.6 + - + +
13F VAL* 3.8 17.5 - - + -
15F ALA* 1.3 78.4 - - - +
17F ILE* 1.3 63.1 + - - +
18F GLY 4.1 11.7 - - - +
20F ILE 3.7 3.1 - - - -
21F VAL* 3.7 21.5 - - + -
67F THR* 4.3 11.9 - - - +
70F LEU* 4.3 20.9 - - + +
71F VAL 6.0 0.2 - - - -
72F ARG* 6.1 0.2 - - + -
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Residues in contact with ILE 17 (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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66B LEU 5.1 0.4 - - - +
67B ASN* 3.9 28.3 - - + +
68B LEU 4.0 10.3 - - - +
69B GLU* 4.7 13.0 - - + +
289B ARG* 4.1 14.6 - - - +
15F ALA* 4.5 9.9 - - + -
16F VAL* 1.3 77.8 - - - +
18F GLY* 1.3 60.9 + - - +
19F ALA 3.0 9.9 + - - -
20F ILE* 3.0 32.3 + - + +
22F ASP* 5.1 1.1 - - - +
60F ARG* 4.7 17.5 - - - +
271F LEU* 4.0 33.6 - - + +
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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