Contacts of the strand formed by residues 168 - 172 (chain A) in PDB entry 2XGZ
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 GLU 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASN* 3.4 19.4 + - - +
154A LEU 3.9 3.4 - - - -
155A ASN* 4.3 2.0 - - - +
166A LEU* 5.4 0.9 - - - +
167A GLN* 1.3 90.0 + - + +
169A PHE* 1.3 67.3 + - - +
170A MET* 3.8 11.8 - - + +
211A GLU* 3.7 18.0 - - - +
245A LEU* 3.5 6.8 - - - +
246A ASP* 3.0 54.7 + - + +
396A LYS* 2.8 35.3 + - - +
1440A PEP 3.6 15.9 - - - +
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASN* 3.7 1.6 - - - -
153A VAL* 2.9 26.0 + - - +
154A LEU* 3.0 33.9 + - + +
156A GLY 4.8 0.9 - - - -
164A LEU* 3.6 36.6 - - + -
166A LEU* 3.6 39.5 - - + -
167A GLN 4.8 0.4 - - - -
168A GLU* 1.3 75.1 - - - +
170A MET* 1.3 62.5 + - - +
221A ALA* 4.2 4.9 - - - -
224A ALA* 3.9 12.8 - - + -
225A LEU* 3.9 25.8 - - + -
228A ILE* 3.5 23.8 - - + -
243A ILE* 5.4 0.4 - - + -
244A GLY 3.7 3.1 - - - +
245A LEU* 3.4 27.4 - - + -
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Residues in contact with MET 170 (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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150A PHE* 3.8 27.8 - - + +
151A LEU 3.1 12.1 - - - +
152A ASN* 3.8 21.5 - - + +
153A VAL* 4.5 0.4 - - - -
168A GLU* 3.8 20.4 - - + +
169A PHE* 1.3 77.4 - - - +
171A ILE* 1.3 65.2 + - - +
228A ILE* 5.6 0.6 - - - +
243A ILE* 3.3 10.6 - - - +
244A GLY* 2.8 41.4 + - - +
245A LEU 3.8 30.5 - - - +
246A ASP* 3.9 4.7 - - + +
293A SER* 6.4 0.4 - - - -
295A GLU* 4.6 3.1 - - + +
370A MET* 5.2 4.0 - - + +
396A LYS* 3.7 29.2 - - + -
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Residues in contact with ILE 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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149A PRO 3.3 3.3 - - - +
150A PHE* 3.5 1.0 - - - -
151A LEU* 2.8 46.3 + - + +
153A VAL* 3.5 29.4 - - + -
170A MET* 1.3 79.4 - - - +
172A ALA* 1.3 61.0 + - - +
173A PRO* 3.8 2.6 - - + +
186A GLY* 3.7 25.1 - - - +
189A VAL* 3.7 31.9 - - + -
228A ILE* 3.7 30.1 - - + -
232A ILE* 4.3 5.2 - - + -
241A ILE* 3.5 19.3 - - + -
242A LYS 3.3 5.2 - - - +
243A ILE* 4.8 0.9 - - + -
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Residues in contact with ALA 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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148A VAL* 3.9 10.1 - - + -
149A PRO 3.7 1.6 - - - -
150A PHE* 3.7 37.5 - - + -
171A ILE* 1.3 74.6 - - - +
173A PRO* 1.3 60.8 - - - +
174A THR* 2.8 17.6 + - + +
241A ILE* 4.2 1.3 - - - -
242A LYS* 2.8 46.8 + - + +
243A ILE 5.3 0.4 - - - -
292A VAL* 4.9 0.2 - - + -
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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