Contacts of the strand formed by residues 115 - 120 (chain B) in PDB entry 4NZD
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL* 4.2 20.0 - - + -
110B THR 3.6 0.7 - - - -
111B PHE* 3.5 37.9 - + + -
114B GLN* 1.3 72.1 - - - +
116B GLN* 1.3 62.8 + - - +
117B ILE* 3.8 7.2 + - + +
165B SER* 3.6 2.1 - - - -
166B LEU* 2.8 45.3 + - + +
167B LEU 4.4 1.3 - - - -
168B PRO* 3.9 26.0 - - + -
171B PHE* 3.7 38.5 - + + +
204B PHE* 4.1 19.7 - + - -
205B GLN 4.8 2.7 - - - -
206B THR* 3.3 13.7 - - + -
207B GLN* 3.0 33.4 + - + +
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Residues in contact with GLN 116 (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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108B THR 3.7 1.6 - - - +
109B VAL* 3.6 2.8 - - - +
110B THR* 2.8 48.8 + - - +
112B SER* 6.0 1.6 - - - +
114B GLN* 3.8 12.9 + - + +
115B TYR* 1.3 71.9 - - - +
117B ILE* 1.3 61.8 + - - +
118B SER* 4.0 6.5 + - - -
163B SER* 3.3 25.8 + - - -
164B VAL 3.6 3.7 + - - +
165B SER* 3.5 25.6 + - - +
24C HIS* 3.9 21.2 + - - -
25C PRO* 4.5 6.3 - - - +
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Residues in contact with ILE 117 (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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107B VAL* 4.1 4.7 - - + -
108B THR 3.5 10.3 - - - +
109B VAL* 4.2 18.2 - - + -
115B TYR* 4.0 13.5 - - + +
116B GLN* 1.3 74.1 - - - +
118B SER* 1.3 62.2 + - - +
119B TRP* 3.7 24.1 - - + -
139B LEU* 4.2 11.0 - - + -
163B SER* 3.4 1.5 + - - -
164B VAL* 2.8 43.5 + - + -
166B LEU* 3.5 38.8 - - + -
171B PHE* 5.0 2.2 - - + -
179B LEU* 4.0 30.3 - - + -
181B VAL* 4.7 0.4 - - + -
204B PHE* 6.4 0.2 - - + -
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Residues in contact with SER 118 (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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106B ASP 4.0 0.2 - - - +
107B VAL* 3.5 2.1 - - - +
108B THR* 2.9 48.5 + - - +
116B GLN* 4.0 6.9 + - - -
117B ILE* 1.3 75.1 - - - +
119B TRP* 1.3 68.1 + - - +
162B ARG 3.2 13.2 - - - -
163B SER* 3.6 16.2 - - - -
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Residues in contact with TRP 119 (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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104B PRO* 3.8 20.4 - - + -
105B PHE 3.8 9.9 - - - +
106B ASP 3.9 5.2 - - - -
107B VAL* 4.0 14.1 - - + -
117B ILE* 3.7 31.4 - - + -
118B SER* 1.3 83.0 - - - +
120B ARG* 1.3 76.1 + - - +
121B SER* 5.3 0.4 - - - -
137B TYR* 3.5 39.4 - + + -
139B LEU* 3.9 17.7 - - + -
157B ILE* 5.4 4.5 - - + -
161B SER 3.4 18.4 - - - -
162B ARG* 3.0 44.6 + - + +
164B VAL* 4.2 16.8 - - + -
181B VAL* 3.8 23.6 - - + -
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Residues in contact with ARG 120 (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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104B PRO* 3.4 9.2 - - - +
105B PHE* 2.9 61.5 + - + +
106B ASP* 4.2 16.6 - - + +
119B TRP* 1.3 81.0 - - - +
121B SER* 1.3 61.3 + - - +
124B GLU* 2.3 42.7 + - - -
162B ARG* 3.3 15.6 - - - +
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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