Contacts of the strand formed by residues 105 - 112 (chain B) in PDB entry 3K3K
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 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.7 43.7 - - + -
46B TRP* 3.4 4.1 - - - -
98B ILE* 3.8 18.0 - - + +
99B LEU* 3.6 0.9 - - - -
100B ASP* 2.9 35.0 + - + +
103B ARG* 3.7 20.9 - - + +
104B ARG* 1.3 80.0 - - - +
106B THR* 1.3 63.8 + - - +
123B VAL* 4.0 10.3 - - + -
124B THR 3.5 4.3 - - - -
125B THR* 3.8 24.2 - - + -
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TRP* 3.9 11.4 - - + -
49B VAL* 3.7 40.0 + - + +
50B ARG* 5.1 0.9 + - - -
52B PHE* 5.7 0.5 - - - -
58B TYR* 5.9 0.4 - - - +
96B LEU* 3.6 13.3 - - - +
98B ILE* 2.9 23.1 + - - -
99B LEU* 3.7 8.5 - - - +
105B VAL* 1.3 75.7 - - - +
107B GLY* 1.3 61.3 + - - +
123B VAL* 3.5 6.9 - - - +
124B THR* 2.9 40.6 + - - +
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Residues in contact with GLY 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU* 3.5 8.3 - - - +
97B ASP* 2.9 26.9 + - - -
98B ILE* 3.2 12.7 + - - +
106B THR* 1.3 81.3 + - - +
108B PHE* 1.3 65.8 - - - +
122B SER 3.0 15.3 - - - -
123B VAL* 4.1 5.8 - - - -
124B THR 4.7 0.4 - - - -
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Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PHE* 3.9 17.7 - + + -
59B LYS* 3.6 21.8 - - - -
79B ARG* 3.7 9.9 - - - -
94B GLU* 3.8 33.9 - - + -
95B ARG 3.2 14.1 - - - +
97B ASP* 3.1 10.9 + - - +
107B GLY* 1.3 77.3 - - - +
109B SER* 1.3 64.0 + - - +
110B ILE* 4.0 14.1 - - + -
120B TYR* 4.0 15.3 - + - -
121B LYS* 3.4 0.5 - - - -
122B SER* 2.9 47.3 + - - -
124B THR* 6.2 0.2 - - - -
141B GLU* 5.0 1.8 - - - -
1001B A8S 3.5 25.8 - - - -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLU* 3.3 0.9 - - - -
95B ARG* 2.8 57.6 + - - -
97B ASP* 2.6 21.3 + - - -
108B PHE* 1.3 75.6 - - - +
110B ILE* 1.3 66.2 + - - +
111B ILE* 3.5 6.7 + - - +
120B TYR 3.3 8.5 - - - -
121B LYS* 3.6 17.5 - - - +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B SER* 3.6 6.3 - - - +
93B THR 3.5 4.5 - - - +
94B GLU* 4.0 15.0 - - + +
108B PHE* 4.0 4.9 - - + -
109B SER* 1.3 73.5 - - - +
111B ILE* 1.3 64.1 + - - +
112B GLY 3.6 7.4 - - - +
115B HIS* 3.0 35.0 - - + +
117B LEU* 4.3 9.6 - - + +
119B ASN* 4.6 8.7 + - - -
120B TYR* 2.9 57.8 + - + +
1001B A8S 3.5 31.0 - - + -
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B THR* 3.9 23.1 - - + -
93B THR* 2.7 41.7 + - + +
94B GLU 4.2 2.9 - - - +
95B ARG* 3.5 37.0 - - + +
109B SER* 3.9 11.0 - - - +
110B ILE* 1.3 79.0 - - - +
112B GLY* 1.3 53.8 + - - +
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B THR* 2.9 33.1 + - - +
110B ILE* 3.6 2.6 - - - +
111B ILE* 1.3 78.9 - - - +
113B GLY* 1.3 59.9 + - - -
115B HIS* 3.2 17.3 - - - -
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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