Contacts of the strand formed by residues 167 - 172 (chain F) in PDB entry 5IJ7
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 167 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ASN* 4.4 4.2 + - - -
524A ASP* 2.6 32.5 + - - +
525A HIS* 3.8 4.1 - - + -
526A PRO* 3.2 33.2 - - + +
99B LYS* 4.8 7.2 - - - +
101B LEU* 4.9 2.5 - - - -
124F TYR* 4.4 1.5 + - - -
161F ILE* 3.6 5.7 - - - +
162F ASN* 2.9 28.7 + - + -
165F THR* 3.2 34.4 - - + +
166F MET* 1.4 78.8 - - - +
168F CYS* 1.3 64.5 + - - +
169F ILE* 3.3 22.7 + - + +
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Residues in contact with CYS 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A HIS 5.7 0.2 - - - -
526A PRO* 4.0 14.0 - - - +
528A GLN* 5.8 2.7 - - + +
101B LEU* 3.9 25.3 - - + +
102B ASN* 5.4 8.6 - - - +
159F ARG* 3.2 44.6 - - - +
160F ILE 3.8 5.2 - - - -
161F ILE* 4.5 2.0 - - - +
167F GLN* 1.3 73.5 - - - +
169F ILE* 1.3 62.1 + - - +
170F LYS 3.4 23.8 - - - -
171F HIS* 4.7 6.1 - - - -
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Residues in contact with ILE 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASN* 5.7 2.2 - - - +
526A PRO* 4.3 14.4 - - + +
527A ARG* 3.5 20.1 + - - -
141F ASP* 6.1 0.7 - - - +
148F LEU* 4.4 12.6 - - + -
160F ILE* 2.8 32.7 + - + +
162F ASN* 3.4 37.0 - - + +
165F THR* 5.0 0.7 - - - +
167F GLN* 3.3 26.5 + - + +
168F CYS* 1.3 73.8 - - - +
170F LYS* 1.4 77.2 + - + +
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Residues in contact with LYS 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A ARG* 3.4 31.2 - - - +
148F LEU* 6.3 2.2 - - + -
160F ILE* 2.9 46.3 + - + -
168F CYS* 3.4 9.4 - - - -
169F ILE* 1.4 91.9 - - + +
171F HIS* 1.4 68.6 + - - +
172F TYR* 3.4 19.5 - - - +
206F ILE* 2.9 23.6 + - + +
207F GLN* 4.0 8.3 + - - +
209F ASP* 2.8 23.0 + - - -
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Residues in contact with HIS 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ARG* 4.2 21.9 + - + +
528A GLN* 5.2 9.7 + - - -
104B VAL* 3.4 48.1 - - + +
157F ILE* 4.4 5.2 - - + -
158F ILE 3.1 14.4 - - - +
159F ARG* 4.5 5.2 - - + -
168F CYS* 4.7 5.8 - - - -
170F LYS* 1.4 80.5 - - - +
172F TYR* 1.3 72.5 + - - +
173F VAL* 4.0 9.4 - - + +
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Residues in contact with TYR 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527A ARG* 5.9 1.3 - - - -
156F GLY 3.9 2.6 - - - +
157F ILE* 3.4 5.8 - - - -
158F ILE* 2.9 58.4 + - + +
160F ILE* 3.9 14.4 - - + -
170F LYS* 3.4 17.9 - - + +
171F HIS* 1.3 79.2 - - - +
173F VAL* 1.3 62.4 + - - +
204F TRP* 3.9 41.0 - + + -
205F ASN 5.1 0.4 - - - -
206F ILE* 3.4 44.7 - - + +
209F ASP* 2.8 48.4 + - + -
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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