Contacts of the strand formed by residues 158 - 163 (chain D) in PDB entry 4ILW
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 ILE 158 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TRP* 4.5 9.6 - - + +
113D LEU* 4.9 4.7 - - + -
114D THR 2.8 13.5 + - - +
115D TYR* 3.1 8.1 - - + +
116D ARG 3.0 24.3 + - - +
137D LEU* 5.4 0.2 - - + -
148D PHE* 4.0 29.6 - - + -
157D ASP* 1.3 80.6 - - + +
159D MET* 1.3 61.1 + - - +
160D ILE* 3.6 23.9 + - + +
192D GLY 3.5 24.5 - - - +
194D ILE* 4.1 14.8 - - + -
219D LEU* 4.2 15.3 - - + -
222D SER* 4.2 10.1 - - - +
223D LEU* 4.7 7.4 - - + -
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Residues in contact with MET 159 (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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35B ILE* 5.0 7.4 - - + -
116D ARG* 3.0 43.3 - - + +
118D VAL* 4.1 17.3 - - + -
154D GLY 3.8 11.7 - - - +
155D GLU* 3.7 17.0 - - - +
156D ALA* 3.2 43.7 - - + +
158D ILE* 1.3 69.2 - - - +
160D ILE* 1.3 61.6 + - - +
161D SER* 4.9 0.8 + - - -
193D ASP* 3.0 33.3 + - + +
194D ILE 3.0 23.2 + - - +
195D HIS* 4.9 1.7 - - - -
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Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D TYR* 4.2 17.3 - - + -
116D ARG 2.9 9.6 + - - +
117D ILE* 3.7 11.3 - - + +
118D VAL* 2.9 28.9 + - - +
119D ASN 4.1 0.3 + - - -
133D ILE* 3.8 37.5 - - + -
137D LEU* 5.8 0.7 - - + -
158D ILE* 3.8 27.4 - - + +
159D MET* 1.3 75.9 - - - +
161D SER* 1.3 61.7 + - - +
162D PHE* 5.8 1.6 - - + -
194D ILE* 3.4 21.3 - - + +
196D PHE* 3.4 34.1 - - + -
219D LEU* 5.2 4.5 - - + -
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Residues in contact with SER 161 (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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118D VAL* 4.4 10.8 - - - -
119D ASN* 3.2 17.9 - - - -
159D MET 4.9 0.9 + - - -
160D ILE* 1.3 77.7 - - - +
162D PHE* 1.3 66.6 + - - +
163D ALA* 5.5 2.1 - - - +
194D ILE 2.9 5.3 + - - +
195D HIS* 3.2 30.2 + - - -
196D PHE* 2.8 34.7 + - - -
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Residues in contact with PHE 162 (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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117D ILE* 5.2 2.2 - - + -
119D ASN* 2.7 56.0 + - - +
120D TYR 4.8 0.9 - - - +
121D THR* 3.6 46.4 - - + +
129D VAL* 4.2 14.8 - - + -
133D ILE* 5.4 1.3 - - + -
160D ILE* 5.8 1.3 - - + -
161D SER* 1.3 76.3 - - - +
163D ALA* 1.3 64.3 + - - +
196D PHE* 3.4 44.0 - + + +
198D ASP* 3.5 18.4 - - - +
202D TRP* 3.8 21.8 - + - -
211D LEU* 4.1 18.6 - - + -
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Residues in contact with ALA 163 (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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161D SER* 4.2 3.7 + - - +
162D PHE* 1.3 75.4 - - - +
164D VAL* 1.3 61.1 + - - +
167D HIS* 3.4 39.9 - - + +
173D PHE* 3.5 7.4 - - + -
195D HIS* 5.4 2.5 - - + -
196D PHE 2.9 10.7 + - - +
197D ASP* 3.2 5.7 - - - -
198D ASP* 2.8 25.1 + - - +
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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