Contacts of the strand formed by residues 173 - 179 (chain P) in PDB entry 1O18
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 GLN 173 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162P ALA* 3.6 25.1 - - + +
165P PHE* 3.7 8.9 + - - +
166P MET* 3.6 14.5 - - + +
169P ASP* 5.2 0.7 - - - +
171P GLU* 2.9 31.1 + - - +
172P ASN* 1.3 79.2 + - - +
174P SER* 1.3 56.4 + - - +
458P PHE* 3.2 8.0 + - - +
459P ILE* 3.6 22.3 - - + -
460P GLY* 3.0 20.9 + - - -
667P THR* 3.0 17.3 + - - +
668P HIS* 2.6 38.6 + - - +
670P HIS* 3.2 25.5 + - + -
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Residues in contact with SER 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173P GLN* 1.3 73.7 - - - +
175P ILE* 1.3 59.8 + - - +
176P LEU* 3.3 13.1 - - - +
249P PHE* 5.5 0.4 - - - -
458P PHE* 6.2 0.2 - - - -
460P GLY* 3.0 15.3 - - - +
462P LEU* 6.3 0.4 - - - -
490P PHE* 5.1 0.7 - - - -
664P LEU* 4.7 14.8 + - - +
667P THR* 2.9 25.9 - - - +
668P HIS 3.2 2.6 + - - -
669P PRO* 3.1 16.1 - - - +
670P HIS* 2.7 39.0 + - - +
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Residues in contact with ILE 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158P ILE* 4.0 21.5 - - + -
159P SER* 4.8 2.0 - - - -
162P ALA* 4.5 9.9 - - + -
174P SER* 1.3 79.5 - - - +
176P LEU* 1.3 66.2 + - - +
177P ILE* 3.5 26.5 - - + -
192P VAL* 4.7 9.6 - - + -
196P PHE* 4.2 18.6 - - + -
459P ILE* 4.2 22.7 - - + -
460P GLY 2.7 9.2 + - - +
461P VAL* 4.3 10.7 - - + +
462P LEU* 3.0 26.5 + - - +
670P HIS* 2.9 7.0 - - + +
672P VAL* 3.8 20.2 - - + -
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Residues in contact with LEU 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174P SER* 3.3 24.0 - - - +
175P ILE* 1.3 79.1 - - - +
177P ILE* 1.4 61.3 - - - +
178P THR* 5.9 0.4 - - - +
462P LEU* 3.6 31.9 - - + -
487P LEU* 4.6 11.0 - - + -
490P PHE* 4.5 10.3 - - + -
664P LEU* 4.4 17.0 - - + -
669P PRO* 4.5 2.7 - - + -
670P HIS 2.7 28.1 + - - +
671P PHE* 4.2 22.2 - - + -
672P VAL 2.8 26.4 + - - +
673P ARG* 3.0 17.8 + - - +
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Residues in contact with ILE 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175P ILE* 3.5 24.0 - - + -
176P LEU* 1.4 69.9 - - - +
178P THR* 1.3 70.8 + - - +
185P LYS* 3.6 23.0 - - + +
188P ASN* 4.8 4.0 - - + -
189P THR* 4.4 22.2 - - + +
192P VAL* 4.4 10.3 - - + -
461P VAL* 4.0 21.1 - - + -
462P LEU* 2.9 22.7 + - - +
463P ASP* 4.0 2.6 - - - -
464P ILE 3.7 13.0 + - - +
672P VAL* 3.3 24.5 - - + -
674P CYS* 3.5 27.1 - - - -
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Residues in contact with THR 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176P LEU* 5.9 0.3 - - - +
177P ILE* 1.3 82.3 + - - +
179P GLY* 1.4 63.4 + - - +
185P LYS* 4.3 3.8 - - - -
462P LEU* 5.7 3.6 - - - +
464P ILE* 3.5 16.0 + - - +
465P ALA 4.2 2.8 + - - -
466P GLY* 4.6 10.8 - - - -
484P ASN* 4.0 14.6 + - - +
487P LEU* 5.4 4.2 - - - +
672P VAL 3.3 4.4 + - - -
673P ARG* 3.6 40.0 + - - +
674P CYS* 2.9 26.3 + - - +
697P CYS 5.8 1.1 - - - +
698P ASN* 4.8 11.5 + - - +
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Residues in contact with GLY 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178P THR* 1.4 78.9 - - - +
180P GLU* 1.3 62.8 + - - -
183P ALA* 4.1 4.7 - - - -
185P LYS* 2.9 25.5 - - - +
464P ILE 4.3 1.6 + - - -
465P ALA* 4.2 1.9 - - - +
466P GLY* 3.8 17.6 + - - +
674P CYS 3.7 15.7 - - - -
698P ASN* 5.4 3.6 - - - -
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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