Contacts of the strand formed by residues 77 - 83 (chain F) in PDB entry 4K81
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 77 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F LYS 3.5 4.9 + - - +
6F LEU* 3.4 15.8 - - - +
7F VAL* 2.8 32.6 + - - +
75F GLY 3.5 0.6 - - - -
76F GLU* 1.3 81.7 - - - +
78F PHE* 1.3 60.6 + - - -
110F PRO* 3.4 14.4 - - - -
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Residues in contact with PHE 78 (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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7F VAL* 3.3 35.4 - - + +
9F VAL* 4.3 5.4 - - + -
71F TYR* 4.2 0.9 - + - -
72F MET* 3.6 45.3 - - + -
75F GLY* 3.8 28.3 - - - -
77F GLY* 1.3 76.3 - - - -
79F LEU* 1.3 61.3 - - - +
80F CYS* 3.7 7.1 + - - -
100F ILE* 3.7 33.0 - - + -
104F LYS* 3.9 4.7 - - + -
109F VAL* 3.9 28.5 - - + -
110F PRO 3.1 6.8 + - - -
111F MET* 3.1 29.0 - - + +
112F VAL 3.2 6.2 + - - +
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Residues in contact with LEU 79 (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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6F LEU* 6.4 1.3 - - + -
7F VAL 2.8 13.1 + - - +
8F VAL* 3.5 30.6 - - + +
9F VAL 2.8 31.0 + - - +
19F LEU* 5.0 11.2 - - + -
77F GLY 4.3 0.2 + - - -
78F PHE* 1.3 71.0 - - - +
80F CYS* 1.3 60.4 + - - +
81F VAL* 3.5 9.9 + - + -
112F VAL* 3.7 19.3 - - + -
114F VAL* 3.7 28.3 - - + -
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Residues in contact with CYS 80 (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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9F VAL* 3.7 22.9 - - + -
78F PHE* 4.3 6.5 - - - -
79F LEU* 1.3 70.1 - - - +
81F VAL* 1.3 60.3 + - - +
93F ILE* 4.2 15.5 - - + +
96F TYR* 5.2 4.5 - - + -
97F ARG* 5.2 2.7 - - - -
100F ILE* 4.2 9.6 - - - -
111F MET* 3.5 38.1 - - + -
112F VAL 3.1 11.5 + - - +
113F LEU* 3.6 15.9 - - + +
114F VAL 2.8 26.2 + - - +
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Residues in contact with VAL 81 (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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8F VAL* 3.8 28.7 - - + -
9F VAL 2.8 13.6 + - - +
10F GLY* 3.3 21.7 - - - -
11F ALA 4.2 1.4 + - - -
14F VAL* 3.8 22.4 - - + +
16F LYS* 4.3 2.7 - - + -
19F LEU* 4.0 19.1 - - + -
79F LEU* 4.0 7.9 - - + +
80F CYS* 1.3 75.9 - - - +
82F PHE* 1.3 72.0 + - - +
89F SER 5.0 0.2 - - - +
93F ILE* 3.5 7.7 - - - +
114F VAL* 3.5 15.5 - - + +
116F ASN* 3.8 22.0 - - + -
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Residues in contact with PHE 82 (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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14F VAL* 4.0 11.2 - - - -
81F VAL* 1.3 78.4 - - - +
83F ALA* 1.3 78.7 + - - +
84F ILE* 4.1 7.2 - - + -
89F SER* 3.7 24.0 - - - +
90F PHE* 3.9 23.8 - + + -
93F ILE* 3.6 23.3 - - + -
113F LEU* 4.2 7.4 - - + -
114F VAL 3.0 28.2 + - - -
115F GLY* 3.7 7.9 - - - -
116F ASN* 3.0 24.1 + - - +
125F VAL* 3.6 31.6 - - + -
130F ALA* 4.0 4.0 - - + -
141F TYR* 3.8 30.7 - + - -
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Residues in contact with ALA 83 (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 GLY 5.1 0.2 - - - +
14F VAL* 3.7 22.9 - - + +
82F PHE* 1.3 84.1 - - - +
84F ILE* 1.3 61.3 + - - +
85F ASN* 3.1 20.4 - - - +
86F ASN* 3.0 29.0 + - + +
89F SER* 3.5 10.1 + - - +
116F ASN 3.6 4.7 - - - -
117F LYS* 4.1 16.4 - - + +
125F VAL* 4.8 0.3 - - - +
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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