Contacts of the strand formed by residues 99 - 104 (chain B) in PDB entry 2XXA
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 PHE 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B LEU* 4.2 8.5 - - + -
92B ASN 3.3 25.1 - - - -
93B VAL* 3.2 48.2 - - + +
94B GLU 4.8 0.9 - - - -
96B LYS* 3.7 30.0 + - + -
98B PRO* 1.3 69.3 - - - +
100B VAL* 1.3 58.8 + - - +
101B ILE* 3.8 19.2 + - + -
182B ASP 3.0 14.9 + - - +
183B VAL* 3.6 5.9 - - + +
184B LEU 2.8 32.4 + - - +
218B HIS* 3.6 32.5 - + + -
219B GLU* 4.0 9.2 - - + -
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Residues in contact with VAL 100 (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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98B PRO* 3.6 17.3 - - + +
99B PHE* 1.3 72.9 - - - +
101B ILE* 1.4 63.4 + - - +
102B LEU* 4.1 1.1 - - - +
173B ILE* 4.5 15.0 - - + -
184B LEU* 3.4 28.0 - - + +
186B ALA* 4.7 8.7 - - + -
209B MET* 3.6 26.0 - - + -
216B ALA* 3.8 17.5 - - + -
217B PRO* 3.8 4.0 - - + -
218B HIS* 2.9 24.4 + - + +
219B GLU 2.9 31.6 + - - +
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Residues in contact with ILE 101 (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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91B LEU* 4.4 3.8 - - + -
93B VAL* 3.7 26.9 - - + -
99B PHE* 3.8 11.9 - - + -
100B VAL* 1.4 78.5 - - - +
102B LEU* 1.3 59.6 + - - +
103B MET* 3.7 4.8 + - - -
118B LEU* 5.5 2.5 - - + -
122B PHE* 4.0 14.4 - - + -
183B VAL* 3.8 21.8 - - + -
184B LEU 3.0 8.1 + - - +
185B ILE* 3.7 20.0 - - + +
186B ALA 3.0 27.9 + - - +
219B GLU* 3.4 19.5 - - + -
221B MET* 3.9 32.5 - - + -
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Residues in contact with LEU 102 (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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100B VAL* 4.1 1.4 - - + -
101B ILE* 1.3 70.3 - - - +
103B MET* 1.3 58.7 + - - +
104B VAL* 3.6 20.3 + - + -
169B ILE* 4.7 1.6 - - + -
186B ALA* 3.9 18.8 - - + -
188B THR* 4.1 14.1 - - + -
202B LEU* 4.9 5.2 - - + -
205B ILE* 3.9 25.8 - - + -
206B VAL* 3.8 28.7 - - + -
209B MET* 4.4 9.4 - - - -
217B PRO* 4.2 13.7 - - + +
219B GLU 2.7 16.5 + - - +
220B VAL* 3.5 7.2 - - + +
221B MET 2.8 31.3 + - - +
243B VAL* 4.5 10.3 - - + -
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Residues in contact with MET 103 (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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101B ILE* 4.4 3.8 - - - +
102B LEU* 1.3 69.6 - - - +
104B VAL* 1.3 54.2 + - - +
111B LYS* 3.5 29.7 - - + +
114B THR* 3.9 21.1 - - + -
115B ILE* 3.7 27.4 - - + -
118B LEU* 4.3 10.8 - - + -
185B ILE* 3.9 9.4 - - + -
186B ALA 3.0 19.2 + - - +
187B ASP* 4.4 4.9 - - - +
188B THR* 2.6 34.5 + - - +
221B MET* 3.5 31.4 - - + +
223B THR* 3.3 25.1 - - - +
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Residues in contact with VAL 104 (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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102B LEU* 4.2 20.2 - - + +
103B MET* 1.3 77.8 - - - +
105B GLY* 1.3 57.2 + - - +
111B LYS* 3.7 5.8 - - - -
188B THR* 3.9 5.4 - - - +
191B ARG* 5.7 0.2 - - - -
202B LEU* 3.6 33.4 - - + -
220B VAL* 4.0 10.3 - - + -
221B MET 2.9 15.7 + - - +
222B LEU* 3.3 5.6 - - + -
223B THR* 3.0 28.6 + - - -
239B PHE* 3.7 24.5 - - + -
243B VAL* 5.6 0.7 - - + -
245B LEU* 3.7 22.0 - - + -
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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