Contacts of the strand formed by residues 255 - 259 (chain A) in PDB entry 2QH5
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 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A LEU* 3.4 16.8 - - + +
138A THR* 4.0 15.0 - - + -
161A VAL* 3.7 46.8 + - + +
164A PHE* 5.2 5.8 - - + -
249A MET* 3.2 43.1 - - + +
252A SER* 3.5 34.8 - - - +
253A HIS 3.5 4.0 + - - -
254A LYS* 1.3 79.4 - - - +
256A LYS* 1.3 79.6 + - - +
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Residues in contact with LYS 256 (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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130A LEU* 4.0 24.9 - - + -
135A PHE* 3.4 46.9 - - + +
136A LEU 3.3 7.1 + - - +
137A VAL* 3.6 3.7 - - + -
138A THR* 3.0 29.1 + - - +
159A LEU* 3.3 24.7 - - + +
160A ASP* 3.2 25.0 + - - +
161A VAL* 4.1 3.6 - - - -
253A HIS 5.6 2.6 + - - -
254A LYS 4.0 1.0 + - - -
255A ILE* 1.3 81.0 + - - +
257A MET* 1.3 61.8 + - - +
159B LEU* 3.8 13.2 - - - -
160B ASP* 3.5 21.7 + - - -
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Residues in contact with MET 257 (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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130A LEU* 4.4 0.2 - - - +
138A THR* 3.4 15.3 - - + +
140A GLY* 3.6 27.4 - - - +
153A ILE* 3.8 21.3 - - + -
155A SER* 3.8 9.4 - - - +
158A GLY 3.5 27.1 - - - +
159A LEU* 2.9 26.2 + - - +
161A VAL* 4.0 12.3 - - + -
183A TYR* 3.7 49.6 - - + -
256A LYS* 1.3 76.7 - - - +
258A VAL* 1.3 70.3 + - - +
259A GLU* 3.9 13.2 - - + +
133B LYS* 5.7 0.2 + - - -
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Residues in contact with VAL 258 (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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123A ALA* 3.8 33.7 - - + +
126A LYS* 4.0 20.6 - - + -
127A ALA* 4.2 11.9 - - + +
130A LEU* 3.8 22.4 - - + -
137A VAL* 3.8 13.7 - - + -
138A THR 3.1 6.2 + - - +
139A PHE* 3.2 17.3 - - + +
140A GLY 2.9 20.5 + - - -
158A GLY 4.7 1.3 - - - -
159A LEU* 5.9 0.2 - - + -
257A MET* 1.3 81.1 - - - +
259A GLU* 1.3 65.5 + - - +
260A LEU 3.6 0.2 + - - -
133B LYS* 6.0 1.6 - - - +
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Residues in contact with GLU 259 (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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119A ALA 5.5 0.5 - - - +
123A ALA* 4.1 8.5 - - - +
140A GLY 3.6 6.7 - - - +
157A ASN 5.1 0.5 - - - +
158A GLY* 4.0 15.6 + - - +
183A TYR* 3.8 36.1 + - + -
257A MET* 3.9 8.3 - - + -
258A VAL* 1.3 82.8 - - - +
260A LEU* 1.3 61.1 + - - +
261A ASN* 3.7 31.6 + - - +
133B LYS* 4.0 16.7 + - - +
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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