Contacts of the strand formed by residues 116 - 122 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LEU* 5.0 2.2 - - + -
104A PHE* 3.5 1.4 - - - -
105A SER* 2.7 45.9 + - - +
114A SER* 2.9 41.2 + - - +
115A ASN* 1.3 78.0 - - - +
117A TRP* 1.3 62.0 + - - +
137A TYR* 4.0 31.3 + + + -
142A PRO* 3.5 41.5 - - + -
143A PHE 3.3 23.3 - - - -
144A ARG* 3.5 44.9 - - + -
145A GLY 4.2 0.9 - - - +
164A MET* 3.7 6.9 - - - +
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Residues in contact with TRP 117 (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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103A LEU* 3.2 15.3 - - - +
116A TRP* 1.3 76.1 - - - +
118A ASN* 1.3 69.4 + - - +
119A VAL* 3.4 34.5 - - + -
142A PRO* 3.2 4.6 - - - +
143A PHE* 2.8 80.6 + + + +
144A ARG 4.1 6.7 + - - -
150A HIS* 3.7 17.3 - + + -
160A SER* 4.9 3.1 - - - -
161A ARG 4.5 0.4 - - - -
162A GLY* 3.3 47.1 - - - -
164A MET* 3.4 36.5 - - + +
172A LEU* 3.7 22.2 - - + -
174A ILE* 4.2 11.7 - - + -
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Residues in contact with ASN 118 (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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101A ALA 4.4 1.1 - - - -
102A VAL* 3.3 5.5 - - - +
103A LEU* 2.9 49.7 + - + +
117A TRP* 1.3 78.0 - - - +
119A VAL* 1.3 79.8 + - - +
120A ARG* 4.9 0.4 - - - -
136A LEU* 2.8 37.1 + - + +
140A ARG* 3.8 17.6 + - - +
142A PRO* 3.5 22.0 - - + +
143A PHE* 4.6 2.5 - - - -
152A ARG* 3.4 21.4 + - - +
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Residues in contact with VAL 119 (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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100A LEU* 4.1 19.3 - - + -
101A ALA 3.5 5.8 - - - +
102A VAL* 4.3 7.2 - - + -
117A TRP* 3.4 27.9 - - + -
118A ASN* 1.3 91.3 + - - +
120A ARG* 1.3 65.8 + - - +
143A PHE* 5.1 3.1 - - + -
152A ARG* 4.2 11.6 + - - -
154A LEU* 3.3 18.5 - - + +
160A SER* 3.6 27.6 + - - +
174A ILE* 3.9 22.7 - - + -
176A VAL* 4.7 5.4 - - + -
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Residues in contact with ARG 120 (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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99A THR 3.8 0.3 - - - +
100A LEU* 3.9 2.6 - - - +
101A ALA* 3.0 33.2 + - - +
118A ASN* 4.4 1.2 + - - -
119A VAL* 1.3 78.1 + - - +
121A VAL* 1.3 75.3 + - - +
122A TYR* 3.9 22.2 - - + -
136A LEU* 3.5 22.6 - - + +
140A ARG* 2.8 61.6 + - - +
152A ARG* 2.5 45.0 - - - +
153A GLY 4.9 5.9 + - - -
154A LEU* 3.9 11.9 + - - +
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Residues in contact with VAL 121 (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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94A MET* 4.1 15.9 - - + -
98A ASN* 4.2 1.3 - - + -
99A THR 3.4 9.0 - - - +
100A LEU* 3.9 13.2 - - + -
120A ARG* 1.3 85.3 - - - +
122A TYR* 1.3 71.6 + - - +
123A LYS 4.3 0.2 + - - -
140A ARG* 6.0 0.2 + - - -
154A LEU* 3.7 42.1 + - + +
156A TYR* 3.3 45.5 + - + -
158A LEU* 4.4 11.7 - - + -
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Residues in contact with TYR 122 (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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98A ASN* 3.1 7.6 - - - +
99A THR* 2.8 40.9 + - + +
101A ALA* 3.9 28.9 - - + -
120A ARG* 3.9 18.2 - - + +
121A VAL* 1.3 79.8 - - - +
123A LYS* 1.3 60.5 + - - +
124A GLY 4.5 0.2 - - - -
126A LYS* 3.9 31.0 - - + -
132A MET* 4.0 20.3 - - + +
135A GLU* 2.7 40.6 + - - +
136A LEU* 3.8 13.6 - - + +
140A ARG* 4.2 20.3 + - - -
156A TYR* 4.6 1.1 - - - -
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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