Contacts of the strand formed by residues 77 - 83 (chain A) in PDB entry 1KI1
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.7 15.0 - - + -
5A LYS 3.2 2.8 + - - +
6A CYS* 3.2 11.8 - - + +
7A VAL 3.0 23.6 + - - -
75A THR* 3.3 8.5 - - - +
76A ASP* 1.3 82.4 - - - +
78A PHE* 1.3 69.6 + - - +
108A THR* 4.2 0.4 - - - -
109A PRO* 3.5 17.0 - - + +
110A PHE* 4.7 1.6 - - - -
111A LEU* 5.0 2.9 - - + -
172A ALA* 3.4 33.4 - - + +
175A ALA* 4.1 16.8 - - + -
176A ALA* 3.3 22.4 - - + +
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.3 28.3 - - + -
9A VAL* 4.2 6.1 - - + -
72A TYR* 3.7 32.5 - + - -
75A THR* 3.8 16.4 - - + -
77A VAL* 1.3 74.7 - - - +
79A LEU* 1.3 67.1 + - - +
80A VAL* 3.8 4.5 - - + -
101A ILE* 3.8 38.1 - - + -
105A CYS* 3.8 28.0 - - + -
108A THR* 3.7 29.8 - - + -
109A PRO 3.2 8.9 + - - -
110A PHE* 3.3 13.6 - - + -
111A LEU 3.0 25.3 + - - -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A CYS* 3.8 15.7 - - - -
7A VAL 2.9 9.6 + - - +
8A VAL* 3.6 18.5 - - + -
9A VAL* 2.9 28.6 + - - +
19A LEU* 5.3 2.7 - - + -
77A VAL* 5.5 0.7 - - + -
78A PHE* 1.3 80.1 - - - +
80A VAL* 1.3 61.9 + - - +
81A CYS* 3.4 6.3 + - - -
111A LEU* 3.7 31.6 - - + -
113A VAL* 3.9 15.9 - - + -
168A VAL* 4.1 12.6 - - + -
169A PHE* 3.6 35.7 - - + -
172A ALA* 3.9 13.9 - - + -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.7 14.1 - - + +
78A PHE* 4.5 1.6 - - + -
79A LEU* 1.3 71.0 - - - +
81A CYS* 1.3 58.7 + - - +
93A VAL* 3.8 33.4 - - + -
97A TRP* 3.9 22.4 - - + -
98A VAL* 4.6 4.9 - - + -
101A ILE* 3.8 28.9 - - + -
110A PHE* 3.8 20.6 - - + -
111A LEU 3.0 12.9 + - - +
112A LEU* 3.6 7.2 - - + +
113A VAL 2.7 29.5 + - - -
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Residues in contact with CYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.6 30.7 - - - -
9A VAL 2.8 14.0 + - - +
10A GLY* 3.5 18.0 - - - -
11A ASP 4.2 3.5 + - - -
14A VAL* 4.0 18.9 - - + +
16A LYS* 4.4 1.8 - - + -
19A LEU* 4.3 13.0 - - + -
79A LEU* 3.8 10.1 - - - -
80A VAL* 1.3 75.8 - - - +
82A PHE* 1.3 64.0 + - - +
89A SER 4.8 0.9 - - - +
93A VAL* 4.3 6.9 - - - +
97A TRP* 5.1 0.2 - - - -
113A VAL* 3.3 26.5 - - - +
115A THR* 4.6 6.3 - - - +
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.2 5.6 - - - -
81A CYS* 1.3 76.4 - - - +
83A SER* 1.3 68.5 + - - +
84A VAL* 3.7 22.0 - - + -
89A SER* 3.6 24.7 - - - +
90A PHE* 3.5 39.7 - + + -
93A VAL* 3.7 6.1 - - + -
112A LEU* 3.3 35.4 - - + -
113A VAL 3.1 6.9 + - - +
114A GLY* 3.8 4.5 - - - -
115A THR* 2.8 27.7 + - - -
137A ILE* 3.8 10.1 - - + -
142A ALA* 3.9 6.3 - - + -
154A TYR* 3.6 34.3 - + - -
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA 5.0 1.3 - - - -
14A VAL* 3.8 13.8 - - - +
82A PHE* 1.3 79.3 - - - +
84A VAL* 1.3 58.5 + - - +
85A VAL* 2.8 22.6 + - - +
86A SER* 2.9 34.7 + - - +
89A SER* 3.2 6.4 + - - -
115A THR* 3.3 14.6 - - - -
116A GLN* 2.6 31.6 + - - +
137A ILE* 4.5 0.5 - - - +
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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