Contacts of the strand formed by residues 92 - 98 (chain A) in PDB entry 1XAI
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 THR 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A PHE* 4.8 1.6 - - - -
33A GLN* 3.3 25.6 + - - +
35A PHE* 3.6 33.4 - - + -
88A VAL* 3.7 9.1 - - + +
89A THR* 3.2 34.1 + - - -
90A ARG 3.4 2.4 - - - -
91A ASN* 1.3 76.7 - - - +
93A ALA* 1.3 75.4 + - - +
94A ILE* 5.1 1.1 - - + -
113A LEU* 4.9 9.2 - - + -
117A VAL* 3.6 8.3 - - - +
118A HIS* 2.9 28.4 + - - +
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Residues in contact with ALA 93 (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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31A PHE* 3.4 37.7 - - + -
33A GLN 3.0 4.6 + - - -
34A SER* 3.3 8.4 - - - +
35A PHE 2.9 25.3 + - - -
92A THR* 1.3 81.2 - - - +
94A ILE* 1.3 65.8 + - - +
95A ILE* 3.6 7.9 - - + +
118A HIS* 3.1 14.6 - - + +
120A ILE* 4.9 3.6 - - + -
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Residues in contact with ILE 94 (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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35A PHE* 3.5 26.7 - - + -
37A LEU* 3.7 29.6 - - + -
83A ILE* 5.0 4.7 - - + -
92A THR* 5.1 0.7 - - + -
93A ALA* 1.3 74.8 - - - +
95A ILE* 1.3 65.2 + - - +
106A ALA* 3.7 25.1 - - + +
109A VAL* 4.9 9.0 - - + -
110A ALA* 3.5 35.0 - - + +
113A LEU* 4.7 14.4 - - + -
117A VAL* 3.9 7.2 - - + -
118A HIS 2.7 8.5 + - - -
119A PHE* 3.4 5.8 - - + -
120A ILE* 2.9 25.8 + - - +
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Residues in contact with ILE 95 (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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24A ILE* 5.2 10.8 - - + -
28A LEU* 4.3 15.9 - - + -
34A SER* 3.9 22.4 - - - +
35A PHE 3.0 8.9 + - - +
36A LEU* 3.6 20.7 - - + +
37A LEU 3.0 26.8 + - - +
59A VAL* 6.4 0.9 - - + -
93A ALA* 3.6 22.7 - - + +
94A ILE* 1.3 80.1 - - - +
96A ALA* 1.3 57.8 + - - +
97A VAL* 3.5 13.9 + - + -
120A ILE* 3.5 17.7 - - + -
122A VAL* 3.5 26.7 - - + -
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Residues in contact with ALA 96 (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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37A LEU 3.7 4.5 - - - -
94A ILE 3.8 2.2 + - - -
95A ILE* 1.3 71.7 - - - +
97A VAL* 1.3 58.9 + - - +
98A GLY 4.0 1.8 - - - +
102A THR* 4.3 2.9 - - - +
103A GLY* 4.2 11.0 - - - +
106A ALA* 3.8 24.5 - - + -
119A PHE* 3.8 7.2 - - + -
120A ILE 2.9 8.6 + - - +
121A GLN* 3.5 24.0 - - - +
122A VAL* 2.8 36.2 + - - +
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Residues in contact with VAL 97 (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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36A LEU* 4.1 15.3 - - + -
37A LEU 3.2 10.5 + - - +
38A ILE* 3.4 33.8 - - + +
39A ASP 3.8 2.6 + - - -
42A VAL* 4.0 4.9 - - + +
50A PHE* 3.4 39.5 - - + -
95A ILE* 3.5 24.7 - - + +
96A ALA* 1.3 78.7 - - - +
98A GLY* 1.3 57.8 + - - +
102A THR* 4.2 3.9 + - - -
122A VAL* 3.4 14.8 - - + +
124A THR* 4.2 13.0 - - + -
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Residues in contact with GLY 98 (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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42A VAL* 4.0 12.1 - - - -
96A ALA 4.0 1.0 - - - -
97A VAL* 1.3 76.4 - - - +
99A GLY* 1.3 69.2 + - - +
102A THR* 3.2 9.9 + - - -
122A VAL 3.5 6.3 + - - -
123A PRO* 3.6 8.1 - - - +
124A THR* 3.3 34.4 + - - +
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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