Contacts of the helix formed by residues 115 - 124 (chain F) in PDB entry 4WYV
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 THR 115 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 4.7 24.2 - - + +
6B ILE* 4.4 17.9 - - + -
113F LEU 4.2 6.7 - - - +
114F VAL* 1.3 79.0 - - - +
116F ARG* 1.3 63.5 + - - +
117F GLU* 3.4 14.0 + - - +
118F ALA* 3.1 30.3 + - + +
119F VAL* 3.2 11.6 + - - +
140F TYR* 3.9 3.6 - - - -
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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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6B ILE* 5.5 2.2 - - + +
10B LEU* 4.1 8.8 - - + +
13B PHE* 3.8 30.9 - - - -
115F THR* 1.3 74.0 - - - +
117F GLU* 1.3 80.4 + - - +
119F VAL* 3.3 5.1 + - - +
120F THR* 3.1 27.4 + - + +
128F ASP* 3.1 30.1 + - - -
135F LEU* 2.9 49.7 + - + +
136F ASP 4.4 2.5 - - - -
137F VAL* 3.9 20.2 - - - +
140F TYR* 3.6 50.5 + - + -
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Residues in contact with GLU 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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1B MET* 5.7 2.8 - - - +
9B GLU* 4.1 18.0 - - - +
13B PHE* 5.4 0.3 - - - -
115F THR* 3.4 15.1 + - - +
116F ARG* 1.3 98.4 + - - +
118F ALA* 1.3 66.1 + - - +
120F THR* 2.5 30.4 + - + +
121F GLU* 3.0 18.8 + - - +
127F PRO* 5.0 9.6 - - + -
129F ARG* 4.8 17.7 - - - +
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Residues in contact with ALA 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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106F VAL* 6.1 0.2 - - + -
114F VAL* 3.7 15.7 - - + -
115F THR* 3.1 27.5 + - + +
117F GLU* 1.3 76.4 - - - +
119F VAL* 1.3 60.2 + - - +
121F GLU* 3.3 14.8 + - - +
122F ILE* 3.1 30.9 + - + +
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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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99F VAL* 4.1 24.5 - - + -
102F ALA* 4.3 11.9 - - + -
114F VAL* 3.3 28.3 - - + -
115F THR 3.3 15.5 - - - +
116F ARG 3.4 7.6 - - - +
117F GLU 3.1 0.2 - - - -
118F ALA* 1.3 73.9 - - - +
120F THR* 1.3 66.0 + - - +
122F ILE* 3.2 17.1 + - - +
123F LEU* 3.2 28.3 + - + +
135F LEU* 4.0 15.9 - - + -
140F TYR* 4.1 14.1 - - + -
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Residues in contact with THR 120 (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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116F ARG* 3.1 19.7 + - + +
117F GLU* 2.5 26.6 + - + +
119F VAL* 1.3 77.0 - - - +
121F GLU* 1.3 64.6 + - - +
123F LEU 3.2 1.9 + - - -
124F GLY 3.2 3.3 + - - -
125F ILE* 3.1 51.0 + - - +
126F GLU 4.0 16.2 - - - +
127F PRO* 4.4 14.3 - - + +
135F LEU* 3.9 25.1 - - + +
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Residues in contact with GLU 121 (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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69F LYS* 4.0 7.8 - - - -
117F GLU* 3.0 20.7 + - - +
118F ALA* 3.6 14.4 - - - +
119F VAL 3.1 0.2 - - - -
120F THR* 1.3 83.7 + - - +
122F ILE* 1.3 65.9 + - + +
124F GLY* 3.2 13.0 + - - +
125F ILE 4.8 3.6 - - - +
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Residues in contact with ILE 122 (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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62F ARG* 4.1 30.1 - - + +
65F PHE* 3.8 42.7 - - + +
69F LYS* 3.3 25.1 + - - +
102F ALA* 4.5 17.9 - - + +
105F VAL* 6.2 0.9 - - + -
106F VAL* 4.4 22.2 - - + -
114F VAL* 4.7 2.0 - - + -
118F ALA* 3.1 22.5 + - + +
119F VAL* 3.2 5.4 + - - +
121F GLU* 1.3 79.6 - - + +
123F LEU* 1.3 57.7 + - + +
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Residues in contact with LEU 123 (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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65F PHE* 4.0 26.2 - - + -
68F VAL* 4.1 13.5 - - + -
69F LYS* 3.6 15.4 - - - +
72F LEU* 3.3 33.2 - - + +
95F LEU* 4.5 20.2 - - + -
98F LEU* 4.0 22.9 - - + +
99F VAL 5.3 0.9 - - - +
102F ALA* 5.6 0.7 - - + -
119F VAL* 3.2 32.9 + - + +
120F THR 3.7 4.3 - - - +
121F GLU 3.2 0.8 - - - -
122F ILE* 1.3 79.8 - - + +
124F GLY* 1.3 60.9 + - - +
125F ILE* 4.1 21.8 - - + -
135F LEU* 5.3 0.9 - - + -
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Residues in contact with GLY 124 (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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69F LYS* 3.8 15.8 - - - +
72F LEU* 5.3 0.9 - - - +
73F THR* 4.6 10.5 - - - +
76F LYS* 3.6 16.6 + - - -
120F THR 3.2 3.2 + - - -
121F GLU* 3.2 13.2 + - - -
122F ILE 3.3 1.2 + - - -
123F LEU* 1.3 79.7 - - - +
125F ILE* 1.3 60.8 + - - +
126F GLU* 4.2 1.2 - - - +
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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