Contacts of the strand formed by residues 157 - 162 (chain A) in PDB entry 4QY2
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 THR 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A TYR* 4.7 3.5 - - - -
121A ILE* 3.7 19.6 - - + +
154A PHE* 3.5 22.0 - - + -
155A PRO* 3.1 20.4 - - + +
156A GLN* 1.3 76.5 + - - +
158A THR* 1.3 69.5 + - - +
159A ASN* 3.3 17.3 + - - -
239A SER* 3.5 2.8 + - - -
240A HIS* 2.9 44.0 + - + +
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Residues in contact with THR 158 (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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156A GLN* 5.6 2.1 + - - +
157A THR* 1.3 80.8 + - - +
159A ASN* 1.3 73.1 + - - +
160A THR* 4.5 4.3 - - - +
237A THR* 3.6 28.0 - - + -
238A PHE 3.2 4.7 - - - +
239A SER* 4.4 10.9 + - - -
212E ALA* 4.9 7.2 - - + -
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Residues in contact with ASN 159 (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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115A PHE* 3.6 37.4 - - + +
116A THR 3.3 26.3 + - - +
117A TYR* 3.4 18.8 - - - -
157A THR* 3.3 8.9 + - - -
158A THR* 1.3 77.1 + - - +
160A THR* 1.3 61.9 + - - +
237A THR* 3.5 0.2 - - - -
238A PHE* 2.6 47.1 + - + +
240A HIS* 3.0 26.3 + - - -
244A LEU* 5.6 0.4 - - + +
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Residues in contact with THR 160 (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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113A THR 5.0 1.9 - - - +
115A PHE* 3.6 10.9 - - - -
158A THR* 4.5 3.6 - - - +
159A ASN* 1.3 73.0 - - - +
161A TYR* 1.3 61.3 + - - +
162A ARG* 3.5 44.0 + - - +
235A ASN* 3.9 15.3 - - + -
236A ILE 3.3 6.7 - - - +
237A THR* 2.8 37.0 + - - +
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Residues in contact with TYR 161 (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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111A ILE* 3.5 9.4 - - + +
112A SER 3.8 18.2 - - - -
113A THR* 4.0 24.5 - - + -
115A PHE* 3.6 20.0 - - + -
160A THR* 1.3 70.9 - - - +
162A ARG* 1.3 77.6 + - - +
163A ASN* 3.8 21.9 + - + -
169A HIS* 2.5 40.7 + - + -
171A ILE* 4.4 5.6 - - + -
230A VAL* 4.4 9.9 - - + -
234A ASP 4.1 0.2 - - - +
235A ASN* 3.4 3.5 - - - -
236A ILE* 2.9 51.8 + - + +
250A VAL* 3.5 27.0 - - + +
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Residues in contact with ARG 162 (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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111A ILE* 5.6 1.2 - - - +
113A THR 5.6 1.4 + - - -
160A THR* 3.5 43.6 + - - +
161A TYR* 1.3 88.4 + - - +
163A ASN* 1.3 59.4 + - - +
164A THR* 3.2 25.4 + - + +
235A ASN* 3.2 26.0 - - - +
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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