Contacts of the helix formed by residues 114 - 121 (chain A) in PDB entry 4WPN
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 LEU 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A GLY 4.0 1.4 + - - -
113A LYS* 1.3 73.2 - - - +
115A TYR* 1.3 60.0 + - - +
116A SER* 4.4 6.7 - - - +
117A ASN* 3.1 36.1 + - - +
118A ALA* 2.8 25.5 + - - +
298A HIS* 5.3 2.1 + - - +
299A GLN* 4.4 12.9 + - - +
335A PRO* 3.6 12.3 - - + +
340A VAL* 3.4 34.3 - - + +
341A THR* 3.4 25.1 - - + +
342A GLN* 3.8 15.0 - - - +
343A GLY 4.0 6.3 - - - +
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Residues in contact with TYR 115 (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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9A LEU* 3.7 24.0 - - + -
10A PRO 2.7 30.0 + - - -
11A VAL* 3.7 20.9 - - + -
12A LEU 4.5 0.2 + - - -
101A LEU* 3.4 19.8 + - - +
104A ALA* 3.8 29.6 - - + -
105A THR* 3.6 19.3 - - - -
108A SER* 3.9 11.2 - - - +
113A LYS 3.2 1.6 + - - -
114A LEU* 1.3 71.8 - - - +
116A SER* 1.3 58.6 + - - +
118A ALA* 4.1 0.7 - - - -
119A TYR* 2.8 40.7 + - + +
335A PRO 2.9 20.0 + - - +
336A LEU* 4.2 25.6 - - + +
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Residues in contact with SER 116 (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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9A LEU* 3.5 31.8 - - - +
114A LEU* 4.4 8.0 - - - +
115A TYR* 1.3 79.7 - - - +
117A ASN* 1.3 67.7 + - - +
120A LEU* 2.9 46.3 + - - +
121A ASN* 5.2 0.2 - - - -
340A VAL 5.6 1.4 + - - -
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Residues in contact with ASN 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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113A LYS* 4.9 6.0 - - + +
114A LEU* 3.1 35.1 + - + +
116A SER* 1.3 83.8 + - - +
118A ALA* 1.3 60.6 + - - +
121A ASN* 2.8 41.3 + - - +
122A ASP* 3.0 13.3 + - - +
297A TYR* 3.7 38.7 + - + +
298A HIS* 5.0 8.7 - - - +
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Residues in contact with ALA 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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104A ALA* 3.6 28.3 - - + +
107A GLU* 4.5 4.0 - - + -
108A SER* 4.4 6.1 - - - +
113A LYS* 3.9 15.7 - - + +
114A LEU 2.8 21.3 + - - +
115A TYR* 3.6 6.5 - - - +
117A ASN* 1.3 71.1 - - - +
119A TYR* 1.3 58.7 + - - +
122A ASP* 3.4 12.0 + - - +
123A LEU* 3.0 35.5 + - - +
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Residues in contact with TYR 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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8A ASP 4.2 1.8 - - - -
9A LEU* 3.7 24.0 - - + -
10A PRO* 3.2 31.6 - - + +
100A ARG* 2.9 78.5 + - + -
101A LEU* 3.7 22.1 - - + +
104A ALA* 3.8 10.8 - - + -
115A TYR* 2.8 41.5 + + + +
118A ALA* 1.3 76.3 - - - +
120A LEU* 1.3 72.2 + - + +
121A ASN 3.6 0.2 - - - -
123A LEU* 3.7 6.9 - - - +
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Residues in contact with LEU 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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8A ASP 3.8 23.8 - - - +
9A LEU* 4.1 11.7 - - + -
100A ARG* 4.0 4.9 + - - +
116A SER* 2.9 34.0 + - - +
119A TYR* 1.3 98.0 - - + +
121A ASN* 1.3 70.6 + - - +
124A ALA* 3.3 19.0 - - - +
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Residues in contact with ASN 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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116A SER 4.9 0.2 + - - -
117A ASN* 2.8 34.7 + - - +
120A LEU* 1.3 84.6 - - - +
122A ASP* 1.3 66.9 + - - +
123A LEU 3.4 0.7 - - - -
124A ALA* 3.4 1.6 + - - +
125A GLY* 2.9 23.2 + - - -
297A TYR* 3.0 30.9 + - - +
601A 3ST 4.0 20.5 - - - +
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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