Contacts of the strand formed by residues 170 - 175 (chain A) in PDB entry 3I5H
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ALA 3.4 20.4 - - - +
162A TYR* 3.7 14.1 - - - +
163A MET* 4.0 15.0 - - + +
166A ASP* 5.6 0.6 + - - -
168A GLU* 2.9 26.3 + - - +
169A ASN* 1.3 72.8 - - - +
171A SER* 1.3 53.2 + - - +
458A PHE* 2.6 12.0 + - - +
459A ILE* 2.6 26.2 - - + -
460A GLY 2.5 32.4 + - - -
665A THR* 4.2 3.4 - - - -
666A HIS* 3.0 36.1 + - - +
668A HIS* 2.6 36.0 + - + -
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Residues in contact with SER 171 (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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170A GLN* 1.3 73.9 - - - +
172A MET* 1.3 63.3 + - - +
173A LEU* 3.8 14.3 - - - +
251A PHE* 3.9 21.1 - - - -
460A GLY 3.3 4.9 - - - +
490A PHE* 4.8 0.3 - - - -
662A LEU* 4.2 3.8 - - - +
665A THR* 2.9 26.1 + - - -
666A HIS 2.9 7.3 + - - -
667A PRO* 3.5 18.4 - - - +
668A HIS* 3.0 30.2 + - - -
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Residues in contact with MET 172 (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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152A LEU* 4.8 1.6 - - + -
155A ILE* 3.8 24.0 - - + -
156A ALA* 4.3 11.7 - - + -
159A ALA* 4.8 1.8 - - + -
171A SER* 1.3 78.2 - - - +
173A LEU* 1.3 60.0 + - - +
174A ILE* 4.6 7.9 - - + -
189A VAL* 3.5 42.4 - - + -
193A PHE* 3.9 14.6 - - - -
459A ILE* 4.4 8.5 - - + -
460A GLY 2.6 16.8 + - - +
461A VAL* 3.0 16.4 - - + +
462A LEU 2.7 27.2 + - - -
668A HIS* 3.3 17.7 - - + +
670A VAL* 3.9 18.6 - - + +
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Residues in contact with LEU 173 (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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171A SER* 3.8 14.4 - - - +
172A MET* 1.3 74.3 - - - +
174A ILE* 1.3 61.0 + - - +
175A THR* 5.8 1.3 - - + -
462A LEU* 3.6 33.7 - - + +
464A ILE* 6.5 0.9 - - + -
487A LEU* 5.0 7.9 - - + +
490A PHE* 4.0 19.7 - - + -
662A LEU* 3.8 24.0 - - + -
667A PRO* 5.1 1.1 - - + -
668A HIS 2.9 12.2 + - - +
669A PHE* 3.4 27.8 - - + -
670A VAL 2.8 22.9 + - - -
671A ARG* 3.0 16.9 + - - +
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Residues in contact with ILE 174 (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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152A LEU* 5.4 0.2 - - + -
172A MET* 4.2 13.5 - - + +
173A LEU* 1.3 77.3 - - - +
175A THR* 1.3 72.7 + - - +
182A LYS* 3.0 34.5 + - + -
185A ASN* 4.5 7.4 - - + -
186A THR* 3.4 36.8 - - - +
189A VAL* 4.8 3.6 - - + -
461A VAL* 3.9 19.5 - - + -
462A LEU 3.5 11.7 + - - +
463A ASP* 4.8 0.2 - - - -
464A ILE* 5.0 2.8 + - - +
670A VAL* 3.0 39.5 - - + -
672A CYS* 4.1 11.7 - - - -
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Residues in contact with THR 175 (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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173A LEU* 5.2 1.1 - - + -
174A ILE* 1.3 80.0 - - - +
176A GLY* 1.3 62.2 + - - +
182A LYS* 4.4 7.6 - - - +
464A ILE* 5.8 9.6 - - + +
466A GLY* 5.9 8.1 - - - -
484A ASN* 6.1 1.3 - - - +
670A VAL 2.8 8.7 + - - -
671A ARG* 2.9 39.6 - - - +
672A CYS* 2.8 27.5 + - - +
696A ASN* 2.8 29.2 + - - +
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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