Contacts of the strand formed by residues 6 - 11 (chain C) in PDB entry 4K71
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 LYS 6 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C THR 4.3 6.5 - - - +
5C PRO* 1.3 77.0 - - - +
7C ILE* 1.3 61.2 + - - +
8C GLN* 5.8 2.2 - - + +
26C TYR 3.7 1.2 - - - +
27C VAL* 3.2 6.2 - - - +
28C SER* 2.8 48.7 + - - +
29C GLY* 5.4 5.2 - - - -
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Residues in contact with ILE 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PRO* 4.2 9.0 - - + +
6C LYS* 1.3 83.3 - - - +
8C GLN* 1.3 68.5 + - - +
25C CYS* 3.8 26.0 - - - -
26C TYR 3.5 2.9 - - - +
27C VAL* 4.4 6.3 - - + -
80C CYS* 4.4 2.7 - - + +
82C VAL* 3.8 35.7 - - + -
87C LEU* 5.6 0.7 - - + -
91C LYS* 4.1 34.1 - - + +
93C VAL* 4.1 34.7 - - + +
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Residues in contact with GLN 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ASP* 3.3 39.5 - - + +
226B PHE 2.9 32.8 + - - +
235B HIS* 4.9 1.7 + - - -
6C LYS* 6.3 2.5 - - + +
7C ILE* 1.3 79.3 - - - +
9C VAL* 1.3 63.0 + - - +
10C TYR* 3.7 26.2 - - + -
24C ASN 3.8 0.5 - - - +
25C CYS* 3.4 4.3 - - - -
26C TYR* 2.9 50.7 + - + +
28C SER* 5.1 3.2 + - - -
93C VAL* 5.4 0.7 - - - -
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Residues in contact with VAL 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.7 0.4 - - + -
8C GLN* 1.3 77.8 - - - +
10C TYR* 1.3 68.9 + - - +
23C LEU* 4.0 13.5 - - + -
24C ASN 3.3 9.6 - - - +
25C CYS* 4.3 2.9 - - + -
39C LEU* 5.8 0.2 - - + -
79C ALA* 5.4 0.7 - - - -
80C CYS* 3.6 33.0 - - + +
93C VAL* 3.6 29.2 - - + +
94C LYS 4.2 9.3 - - - +
95C TRP* 3.8 35.8 - - + +
96C ASP 5.0 3.1 + - - +
99C MET* 4.6 9.2 - - - +
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Residues in contact with TYR 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PHE* 5.5 0.2 - - + -
227B GLY* 3.1 18.6 - - - -
228B PRO* 2.7 27.8 + - - +
229B ASN* 3.9 0.9 - - - -
235B HIS* 3.4 60.1 - + + +
8C GLN* 3.7 36.6 - - + -
9C VAL* 1.3 81.5 - - - +
11C SER* 1.3 56.5 - - - +
23C LEU* 4.2 5.6 - - - -
24C ASN* 2.8 66.1 + - + +
26C TYR* 3.5 16.8 - - + +
95C TRP* 4.1 8.1 - - - +
99C MET* 5.3 3.8 - - - +
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Residues in contact with SER 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PHE* 3.4 23.4 - - - -
229B ASN* 4.3 0.3 - - - +
235B HIS* 4.0 0.9 - - - -
10C TYR* 1.3 84.9 - - - +
12C ARG* 1.3 64.5 + - - +
13C HIS 2.6 23.4 + - - -
15C ALA* 4.1 6.6 + - - +
21C ASN* 4.1 8.3 - - - -
22C PHE 3.3 13.0 - - - -
23C LEU* 4.4 1.3 - - - +
24C ASN* 4.0 2.0 - - - -
70C PHE* 4.3 7.2 - - - -
95C TRP* 3.9 26.1 + - - +
98C ASP* 4.9 1.4 + - - -
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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