Contacts of the helix formed by residues 116 - 122 (chain D) in PDB entry 1EVW
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 ALA 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D THR 4.1 7.1 + - - +
95D THR* 5.0 12.5 + - + +
115D SER* 1.3 73.4 - - - +
117D ASP* 1.3 67.0 + - - +
119D ASN* 3.7 6.4 + - - +
120D LYS* 3.2 26.3 + - - +
13G A 6.4 0.9 - - + +
10H T 6.3 3.1 - - - -
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Residues in contact with ASP 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C TRP* 3.6 20.6 - - + +
144C LEU* 4.1 24.6 - - + +
92D LYS* 5.0 13.1 + - + -
115D SER* 3.3 7.4 + - - +
116D ALA* 1.3 78.0 - - - +
118D ASP* 1.3 67.8 + - - +
120D LYS* 3.0 10.5 + - - +
121D GLY 2.9 19.2 + - - -
11H A 5.3 14.9 - - - +
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Residues in contact with ASP 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C TRP* 5.4 3.0 + - - +
148C GLY* 3.3 23.0 - - - -
149C ALA* 3.8 19.8 + - - +
150C THR* 4.6 4.9 + - - +
89D ILE* 6.0 0.3 - - - +
114D GLU* 3.8 24.5 - - + +
115D SER* 2.7 25.1 + - - +
117D ASP* 1.3 80.1 - - - +
119D ASN* 1.3 66.8 - - - +
121D GLY* 3.2 9.8 + - - +
122D ARG* 3.4 15.7 + - - +
134D HIS* 4.4 11.3 + - + +
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Residues in contact with ASN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D THR* 4.1 5.7 + - - +
96D ALA 3.9 2.8 + - - -
97D SER* 3.1 33.8 + - - +
98D HIS 5.0 0.2 - - - +
101D HIS* 5.2 0.2 - - - -
114D GLU* 3.6 4.4 + - + -
115D SER 3.2 15.4 + - - +
116D ALA* 3.7 8.0 - - - +
117D ASP 3.2 0.2 - - - -
118D ASP* 1.3 80.4 - - - +
120D LYS* 1.3 62.8 + - - +
122D ARG* 3.4 16.5 + - - +
123D ASN* 4.1 1.4 + - - -
13G A 4.7 3.9 + - - +
14N G 2.9 39.2 + - - -
602N MG 2.3 31.0 - - - -
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Residues in contact with LYS 120 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C LYS* 4.6 27.6 - - + +
124C TRP* 4.2 16.8 - - + -
116D ALA* 3.2 12.2 + - + +
117D ASP* 3.0 14.2 + - - +
119D ASN* 1.3 79.6 + - - +
121D GLY* 1.3 59.7 + - - +
123D ASN* 2.8 44.8 + - - +
124D TRP* 3.6 11.7 - - + -
12G A 4.4 36.0 + - - -
13G A 4.7 17.3 + - - +
10H T 6.1 0.2 - - - -
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Residues in contact with GLY 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C TRP* 3.6 41.6 - - - +
117D ASP 2.9 11.5 + - - -
118D ASP* 3.2 5.3 + - - -
120D LYS* 1.3 70.7 - - - +
122D ARG* 1.3 57.1 + - - +
123D ASN 2.8 11.6 + - - -
124D TRP* 3.0 15.8 + - - +
125D CYS* 3.6 6.4 + - - +
134D HIS* 4.4 7.5 - - - -
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Residues in contact with ARG 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C THR* 3.3 12.1 + - - -
97D SER* 3.9 5.8 - - - -
98D HIS 4.8 4.0 - - - -
99D LEU* 3.8 25.3 - - - +
101D HIS* 3.8 15.9 + - + +
112D CYS* 4.2 2.2 - - - -
114D GLU* 2.8 43.5 + - - -
118D ASP 3.4 6.8 + - - +
119D ASN 3.5 8.3 - - - +
120D LYS 3.2 0.6 - - - -
121D GLY* 1.3 73.4 - - - +
123D ASN* 1.3 61.3 + - - +
124D TRP 3.2 1.3 + - - -
125D CYS* 3.2 13.7 + - - +
134D HIS* 3.4 42.7 - - + +
136D VAL* 2.9 35.2 + - - +
137D VAL 3.9 4.9 + - - -
138D CYS* 3.6 21.4 - - - -
142D GLY* 3.3 12.8 + - - -
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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