Contacts of the strand formed by residues 115 - 119 (chain F) in PDB entry 3KTM
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 TYR 115 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F GLN* 3.2 3.5 - - - +
34F ILE* 2.7 42.2 + - + +
35F ALA* 6.0 0.4 - - - -
36F MET* 3.8 17.7 - - + -
66F LYS* 3.6 25.6 + - - -
69F ILE* 3.4 49.9 - - + +
73F CYS* 5.5 0.2 - - - -
85F VAL* 4.6 10.1 - - + -
86F VAL 3.6 4.9 - - - -
87F GLU* 3.6 41.8 + - + +
113F ILE* 4.2 9.6 - - + -
114F PRO* 1.3 75.5 - - - +
116F ARG* 1.3 64.8 + - - +
117F CYS* 3.6 1.7 + - - -
177F ASP* 4.2 1.1 - - - -
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Residues in contact with ARG 116 (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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81C GLN* 4.4 7.7 + - - -
120C GLY* 5.7 0.8 - - - -
121C GLU* 3.2 38.3 + - - +
31F GLU* 3.1 41.5 + - - +
32F PRO 4.0 0.2 - - - -
33F GLN* 3.9 14.8 - - + +
85F VAL* 3.3 8.0 - - - +
86F VAL* 2.8 54.4 + - + +
87F GLU 5.1 1.4 + - - -
88F ALA* 4.1 20.6 - - + +
115F TYR* 1.3 73.1 - - - +
117F CYS* 1.3 60.3 + - - +
118F LEU* 3.3 17.3 + - + +
125F ASP* 2.9 41.8 + - - -
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Residues in contact with CYS 117 (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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31F GLU* 4.9 3.9 - - - +
32F PRO* 2.9 33.9 + - + +
33F GLN* 3.8 8.3 - - - -
34F ILE* 3.4 19.3 - - - -
73F CYS* 2.1 49.6 - - + -
77F TYR* 3.7 12.1 - - - -
82F ILE* 3.8 18.8 - - + -
84F ASN 3.8 3.4 - - - -
116F ARG* 1.3 71.2 - - - +
118F LEU* 1.3 64.4 + - - +
119F VAL* 3.5 3.6 + - - +
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Residues in contact with LEU 118 (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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81C GLN* 6.0 0.4 - - - +
31F GLU* 4.4 5.8 - - - +
82F ILE* 3.4 5.5 - - - -
83F THR* 2.9 28.5 + - - +
84F ASN* 2.8 37.3 + - + +
85F VAL 4.3 2.9 - - - +
86F VAL* 3.7 33.0 - - + -
116F ARG* 3.3 28.7 + - - +
117F CYS* 1.3 71.9 - - - +
119F VAL* 1.3 61.7 + - - +
120F GLY 5.9 0.2 - - - +
122F PHE* 3.9 35.4 - - + -
179F PHE* 4.8 2.9 - - + -
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Residues in contact with VAL 119 (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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28F LEU* 5.5 6.3 - - + -
32F PRO* 4.0 15.9 - - + -
80F LEU* 4.5 13.0 - - + -
81F GLN* 3.6 20.2 - - + +
82F ILE* 3.7 23.8 - - + -
117F CYS 3.5 6.7 + - - +
118F LEU* 1.3 74.3 - - - +
120F GLY* 1.3 73.5 + - - +
121F GLU 3.7 7.8 + - - +
122F PHE* 5.3 0.7 - - - -
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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