Contacts of the strand formed by residues 101 - 106 (chain A) 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 ALA 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU 4.1 11.4 - - - +
96A ALA* 4.9 6.7 - - - -
98A GLN* 5.1 4.7 - - + +
99A PRO 2.7 8.6 + - - +
100A PRO* 1.4 71.0 - - - +
102A VAL* 1.3 55.9 + - - +
103A VAL* 4.0 1.7 + - + -
185A ASP 3.0 17.1 + - - +
186A VAL* 3.4 15.3 - - + +
187A LEU* 2.7 33.4 + - - +
215A VAL* 3.7 22.9 - - + -
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Residues in contact with VAL 102 (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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100A PRO 3.9 3.6 - - - +
101A ALA* 1.3 75.3 - - - +
103A VAL* 1.3 64.5 + - - +
104A LEU 4.0 0.2 - - - -
176A LEU* 3.6 30.5 - - + -
187A LEU* 3.6 9.4 - - + +
189A VAL* 4.1 15.3 - - + -
212A ILE* 3.7 35.9 - - + -
213A ASN 3.5 23.1 + - - +
214A PRO* 3.4 10.4 - - + +
215A VAL* 3.0 30.4 + - - +
216A GLU 3.4 5.0 + - - -
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Residues in contact with VAL 103 (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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94A ASN* 5.0 11.4 - - + +
95A LEU 5.8 0.7 - - - +
101A ALA* 4.9 2.0 - - + +
102A VAL* 1.3 78.1 - - - +
104A LEU* 1.3 62.5 + - - +
105A MET* 4.4 5.3 - - + +
120A LEU* 4.7 12.1 - - + -
124A LEU* 5.8 1.8 - - + -
186A VAL* 4.6 14.8 - - + -
187A LEU 2.9 12.8 + - - +
188A LEU* 3.8 19.9 - - + -
189A VAL* 2.9 29.2 + - - +
215A VAL* 5.1 2.5 - - + -
216A GLU* 3.3 24.2 - - + +
218A LEU* 3.7 30.1 - - + -
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Residues in contact with LEU 104 (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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102A VAL 4.0 1.8 - - - -
103A VAL* 1.3 72.1 - - - +
105A MET* 1.3 62.1 + - - +
106A ALA* 4.2 1.7 + - + +
189A VAL* 3.8 27.1 - - + -
191A THR* 3.9 14.6 - - + -
205A ILE* 3.8 22.7 - - + -
208A VAL* 3.8 19.1 - - + -
209A HIS* 3.9 40.2 - - + +
212A ILE* 4.4 6.3 - - + -
214A PRO* 3.8 17.4 - - + +
216A GLU 3.0 7.3 + - - +
217A THR* 3.6 11.0 - - + +
218A LEU* 3.0 28.6 + - - +
240A LEU* 4.7 0.7 - - + -
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Residues in contact with MET 105 (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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103A VAL* 4.4 8.7 - - + +
104A LEU* 1.3 75.5 - - - +
106A ALA* 1.3 54.2 + - - +
113A LYS* 4.1 11.5 - - + +
116A SER* 3.8 14.4 - - - +
117A VAL* 3.4 30.3 - - + -
120A LEU* 3.8 18.2 - - + -
188A LEU* 6.2 1.6 - - + -
189A VAL 3.0 20.6 + - - +
190A ASP* 4.6 3.4 - - - -
191A THR* 2.6 35.7 + - - +
218A LEU* 3.5 44.0 - - + -
220A VAL* 3.7 23.6 - - + -
246A VAL* 4.1 7.2 - - + -
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Residues in contact with ALA 106 (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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104A LEU* 4.2 4.9 - - + -
105A MET* 1.3 75.3 - - - +
107A GLY* 1.3 56.9 + - - +
113A LYS* 4.3 4.9 - - - +
191A THR* 3.9 5.2 - - - +
194A ARG* 4.5 2.2 - - - -
205A ILE* 3.8 29.8 - - + -
217A THR* 5.6 4.9 - - + -
218A LEU 3.2 7.9 + - - +
219A PHE* 3.3 12.9 - - - -
220A VAL* 3.1 22.3 + - - +
236A PHE* 4.2 13.9 - - + -
240A LEU* 4.7 5.6 - - + -
242A LEU* 5.9 2.5 - - + -
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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