Contacts of the strand formed by residues 112 - 117 (chain D) in PDB entry 2W7U
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 ARG 112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D GLU* 2.7 39.6 + - - -
3D ASN* 5.4 1.4 - - - +
110D LYS 3.8 3.3 + - - +
111D ASP* 1.3 74.8 - - - +
113D ILE* 1.3 63.0 + - - +
132D THR* 4.0 18.6 + - - +
133D GLY 3.6 8.2 + - - -
134D THR* 3.4 20.8 + - - -
160D ASN* 4.1 14.2 - - - +
161D SER* 4.3 10.1 + - - -
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Residues in contact with ILE 113 (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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111D ASP* 4.2 2.0 - - + +
112D ARG* 1.3 81.0 + - - +
114D SER* 1.3 61.5 + - - +
115D VAL* 4.1 10.5 - - + -
132D THR* 3.4 7.3 - - - +
133D GLY 2.9 45.5 + - - +
134D THR* 4.0 2.7 - - - +
135D ILE* 3.8 29.6 - - + -
145D PHE* 3.9 35.0 - - + -
147D ALA* 4.3 2.5 - - + -
158D VAL* 3.9 16.6 - - + -
159D LEU 3.3 7.0 - - - +
160D ASN* 4.7 0.9 - - + -
166D ILE* 3.7 29.6 - - + -
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Residues in contact with SER 114 (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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113D ILE* 1.3 75.8 - - - +
115D VAL* 1.3 63.5 + - - +
116D ILE* 4.1 2.9 + - - +
130D GLU* 3.4 29.4 + - - -
131D SER 3.5 4.5 - - - -
132D THR* 4.1 12.1 - - - +
157D PRO 3.7 1.0 - - - +
158D VAL* 3.6 3.3 - - - -
159D LEU* 2.9 50.1 + - - +
160D ASN 4.4 5.0 + - - -
163D HIS* 5.3 4.5 - - - -
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Residues in contact with VAL 115 (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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113D ILE* 4.1 8.3 - - + -
114D SER* 1.3 76.3 - - - +
116D ILE* 1.3 63.3 + - - +
117D GLY 4.1 0.3 + - - -
129D PHE 3.7 1.7 - - - +
130D GLU* 3.5 1.2 - - - -
131D SER* 2.6 47.1 + - - +
145D PHE* 3.7 26.7 - - + -
147D ALA* 4.0 15.9 - - + -
148D TYR 5.5 2.5 - - - +
149D ALA* 5.9 0.9 - - + -
153D ASN* 4.3 12.5 - - - +
156D SER* 3.7 24.0 - - - +
157D PRO 3.6 5.4 - - - +
158D VAL* 4.3 9.2 - - + -
169D LEU* 4.5 13.5 - - + -
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Residues in contact with ILE 116 (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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14D PRO* 4.7 4.0 - - + +
15D TYR* 3.8 27.4 - - + -
18D VAL* 3.8 22.2 - - + +
25D THR* 3.8 1.4 - - - +
114D SER* 4.8 3.1 - - - +
115D VAL* 1.3 78.8 - - - +
117D GLY* 1.3 60.8 + - - +
128D MET* 3.7 31.9 - - + -
129D PHE 3.4 9.6 - - - +
130D GLU* 3.8 22.2 - - + +
153D ASN* 4.6 0.2 - - - -
156D SER* 3.3 4.9 - - - -
157D PRO* 3.2 34.8 + - + +
159D LEU* 3.8 28.7 - - + -
163D HIS* 6.2 0.7 - - + -
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Residues in contact with GLY 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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18D VAL* 4.7 0.7 - - - -
25D THR* 3.6 10.1 - - - -
115D VAL 4.1 0.2 + - - -
116D ILE* 1.3 76.3 - - - +
118D TYR* 1.3 67.7 + - - -
119D PRO* 3.4 7.2 - - - +
128D MET* 3.7 3.8 - - - +
129D PHE 3.1 30.2 + - - -
153D ASN* 3.5 6.1 + - - -
156D SER* 3.3 16.4 - - - -
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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