Contacts of the strand formed by residues 116 - 122 (chain F) in PDB entry 3ZWG
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 TRP 116 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103F LEU* 5.1 2.0 - - + -
104F PHE* 3.5 2.3 - - - -
105F SER* 2.7 46.9 + - - +
114F SER* 2.9 42.0 + - - +
115F ASN* 1.3 77.1 - - - +
117F TRP* 1.3 60.3 + - - +
137F TYR* 4.0 30.9 + + + -
142F PRO* 3.5 41.7 - - + -
143F PHE 3.3 22.7 - - - -
144F ARG* 3.5 44.9 - - + -
145F GLY 4.2 0.9 - - - +
164F MET* 3.6 7.7 - - - +
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Residues in contact with TRP 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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103F LEU* 3.1 15.9 - - - +
104F PHE* 4.7 0.2 - - - -
116F TRP* 1.3 74.3 - - - +
118F ASN* 1.3 63.0 + - - +
119F VAL* 3.4 33.4 - - + -
142F PRO* 3.3 4.3 - - - +
143F PHE* 2.9 80.5 + + + +
144F ARG 4.1 6.5 + - - -
150F HIS* 3.7 16.0 - + + -
160F SER* 4.9 3.4 - - - -
161F ARG 4.5 0.2 - - - -
162F GLY* 3.4 48.5 - - - -
164F MET* 3.4 37.2 - - + +
172F LEU* 3.7 20.6 - - + -
174F ILE* 4.0 12.3 - - + -
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Residues in contact with ASN 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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101F ALA 4.5 0.4 - - - -
102F VAL* 3.4 5.5 - - - +
103F LEU* 2.9 49.4 + - + +
117F TRP* 1.3 76.6 - - - +
119F VAL* 1.3 82.0 + - - +
120F ARG* 4.6 0.6 - - - +
136F LEU* 2.8 37.8 + - + +
140F ARG* 3.7 18.4 + - - +
142F PRO* 3.5 20.7 - - - +
143F PHE* 4.6 2.4 - - - -
152F ARG* 3.4 23.1 + - - -
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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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100F LEU* 4.1 20.4 - - + -
101F ALA 3.5 6.1 - - - +
102F VAL* 4.2 7.0 - - + -
117F TRP* 3.4 27.9 - - + -
118F ASN* 1.3 91.9 + - - +
120F ARG* 1.3 65.8 + - - +
143F PHE* 5.1 2.6 - - + -
152F ARG* 4.1 11.6 + - - -
154F LEU* 3.3 17.9 - - + +
160F SER* 3.6 29.5 + - - +
174F ILE* 3.8 22.7 - - + -
176F VAL* 4.7 4.9 - - + -
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Residues in contact with ARG 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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99F THR 3.8 0.2 - - - +
100F LEU* 3.9 2.0 - - - +
101F ALA* 3.0 35.0 + - - +
118F ASN* 4.4 1.2 + - - +
119F VAL* 1.3 77.9 + - - +
121F VAL* 1.3 76.5 + - - +
122F TYR* 3.9 20.9 - - + -
136F LEU* 3.5 21.7 - - + +
140F ARG* 2.9 61.6 + - - +
152F ARG* 2.5 44.2 - - - +
153F GLY 4.8 6.1 + - - -
154F LEU* 3.9 9.9 + - - +
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Residues in contact with VAL 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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94F MET* 4.1 15.9 - - + -
98F ASN* 4.2 1.6 - - + -
99F THR 3.4 8.5 - - - +
100F LEU* 3.9 12.3 - - + -
120F ARG* 1.3 83.8 - - - +
122F TYR* 1.3 71.5 + - - +
123F LYS 4.2 0.2 + - - -
154F LEU* 3.6 42.7 + - + +
156F TYR* 3.3 47.2 + - + -
158F LEU* 4.4 12.8 - - + -
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Residues in contact with TYR 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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98F ASN* 3.1 7.4 - - - +
99F THR* 2.8 43.4 + - + +
101F ALA* 3.9 28.9 - - + -
120F ARG* 3.9 17.9 - - + +
121F VAL* 1.3 80.4 - - - +
123F LYS* 1.3 61.1 + - - +
126F LYS* 3.9 32.8 - - + -
132F MET* 4.0 20.6 - - + +
135F GLU* 2.7 42.5 + - - +
136F LEU* 3.8 14.9 - - + +
140F ARG* 4.3 18.9 + - - -
156F TYR* 4.5 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