Contacts of the strand formed by residues 177 - 181 (chain B) in PDB entry 2XML
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 TYR 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ASP* 3.9 18.6 - - + -
138B ILE 3.1 21.5 - - - +
139B ASN* 3.3 26.2 + - - -
140B GLY 3.9 0.2 - - - -
172B GLY* 3.6 12.5 + - - -
173B VAL* 5.3 2.5 - - - -
175B THR* 3.4 43.2 + - - -
176B PRO* 1.3 74.1 - - - +
178B LEU* 1.3 64.2 + - - +
179B TYR* 3.6 29.4 - - + +
288B ALA 3.8 0.2 - - - +
289B GLU* 3.1 6.6 - - - +
290B SER* 2.9 36.8 + - - +
291B THR* 5.4 1.8 - - - -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.8 22.0 - - + -
135B GLY 3.7 2.3 - - - +
137B ASP 3.5 7.3 + - - -
138B ILE* 2.7 44.0 + - + +
139B ASN 5.2 0.2 - - - +
140B GLY* 3.5 25.6 - - - +
141B SER 4.6 0.4 - - - +
142B ILE* 3.5 37.2 - - + +
177B TYR* 1.3 71.6 - - - +
179B TYR* 1.3 63.2 + - - +
180B PHE* 4.1 16.4 - - + -
287B CYS* 4.7 2.0 - - - -
288B ALA 3.3 4.5 - - - +
289B GLU* 3.7 35.7 - - + +
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR* 4.0 23.5 - + + +
135B GLY 3.4 4.3 - - - -
136B ALA* 3.6 14.1 - - + -
137B ASP* 2.6 45.9 + - - -
177B TYR* 3.6 30.4 - - + +
178B LEU* 1.3 75.9 - - - +
180B PHE* 1.3 64.2 + - - +
181B GLY 3.7 1.8 + - - -
200B ASN* 5.4 0.9 - - - -
208B LYS* 5.2 1.2 + - - +
286B ASN* 4.3 1.6 - - - +
287B CYS* 3.4 3.2 + - - -
288B ALA* 2.7 50.7 + - + +
290B SER* 3.1 27.8 + - - -
601B OGA 4.3 18.4 - - - +
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Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.9 18.4 - - + -
67B LEU* 4.0 13.7 - - + -
69B ILE* 4.4 4.9 - - + -
96B VAL* 3.6 42.2 - - + -
99B PHE* 3.3 23.5 - - + -
134B TYR* 3.1 3.7 - - - -
135B GLY* 2.8 41.0 + - - +
138B ILE* 3.8 29.6 - - + -
178B LEU* 4.1 13.7 - - + -
179B TYR* 1.3 72.7 - - - +
181B GLY* 1.3 61.7 + - - +
204B PHE* 4.3 1.8 - + - -
285B PHE* 4.5 5.4 - + - -
286B ASN 3.2 8.7 - - - +
287B CYS* 3.4 38.6 - - + -
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 3.6 10.6 - - - -
134B TYR* 3.6 17.0 - - - -
179B TYR 3.7 1.2 + - - -
180B PHE* 1.3 74.9 - - - +
182B MET* 1.3 60.0 + - - -
185B THR* 3.6 5.8 - - - -
282B ASN* 3.7 2.5 - - - -
284B GLY 3.6 5.2 - - - -
285B PHE* 3.1 21.8 - - - -
286B ASN* 3.1 22.7 + - - -
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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