Contacts of the strand formed by residues 102 - 109 (chain A) in PDB entry 1IAO
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 PRO 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A SER* 5.9 0.9 - - - -
100A GLY 3.4 10.1 - - - +
101A GLN* 1.4 98.9 + - + +
103A ASN* 1.3 60.4 + - - +
153A PHE 3.2 8.3 - - - +
154A ILE* 4.0 17.2 - - + -
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Residues in contact with ASN 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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93A PRO* 4.3 6.8 - - - +
94A LYS* 3.8 1.8 - - - +
95A SER* 3.1 54.0 + - - +
96A PRO 3.5 15.6 - - - +
97A VAL* 3.9 7.4 - - - +
101A GLN* 3.9 7.3 + - - +
102A PRO* 1.3 76.1 - - - +
104A THR* 1.3 81.4 + - - +
152A THR* 3.3 3.6 - - - -
153A PHE* 2.4 68.8 + - + +
155A PRO* 4.7 2.0 - - + -
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Residues in contact with THR 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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93A PRO* 3.7 1.2 - - - +
94A LYS* 3.1 46.8 + - + +
103A ASN* 1.3 80.3 + - - +
105A LEU* 1.3 60.3 + - - +
106A ILE* 4.9 0.7 - - + -
150A TYR* 3.6 37.9 - - + -
151A LEU 2.7 17.7 - - - +
152A THR* 4.2 12.7 - - + +
153A PHE* 3.5 3.6 - - - -
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Residues in contact with LEU 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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91A VAL* 3.6 18.6 - - + -
92A PHE* 3.4 8.1 - - - -
93A PRO* 3.3 31.4 - - + -
104A THR 1.3 67.4 - - - -
106A ILE* 1.3 60.3 - - - +
121A TRP* 3.1 16.6 - - + -
150A TYR* 3.1 3.5 - - - -
151A LEU* 2.3 51.1 + - + +
153A PHE* 3.2 21.6 - - + -
161A TYR* 4.0 25.4 - - + -
178A TRP* 3.2 42.4 - - + -
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Residues in contact with ILE 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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90A THR 3.3 1.3 - - - +
91A VAL* 2.9 5.2 - - - +
92A PHE* 2.6 78.8 + - + +
94A LYS* 3.6 29.4 - - + -
104A THR 4.2 4.9 - - - +
105A LEU* 1.3 78.0 - - - +
107A CYS* 1.3 64.2 + - - +
121A TRP* 3.8 2.7 - - - -
148A LEU* 3.9 22.7 - - + -
149A SER 3.3 9.2 - - - +
150A TYR* 3.6 27.1 - - + -
150B ASN* 4.0 14.8 - - + +
152B ASP* 5.0 0.2 - - - +
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Residues in contact with CYS 107 (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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89A ALA* 3.8 20.6 - - - -
90A THR 3.1 2.9 - - - -
91A VAL* 4.0 6.1 - - + +
106A ILE* 1.3 74.8 - - - +
108A PHE* 1.3 61.8 + - - +
109A VAL* 3.7 6.9 + - - +
119A ILE* 5.6 0.4 - - + +
121A TRP* 3.7 16.5 - - + -
147A LYS 3.6 2.3 - - - +
148A LEU* 3.3 8.1 - - - -
149A SER* 3.1 33.6 + - - +
163A CYS* 2.0 50.3 - - - -
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Residues in contact with PHE 108 (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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88A GLN 3.3 2.0 - - - +
89A ALA* 2.9 4.0 - - - -
90A THR* 2.5 53.9 + - + +
92A PHE* 3.9 18.2 - + + -
106A ILE 4.1 0.4 - - - -
107A CYS* 1.3 70.1 - - - +
109A VAL* 1.3 60.3 + - - +
110A ASP* 3.3 36.6 - - + -
146A HIS* 3.7 27.6 - + + -
147A LYS 4.0 1.1 - - - -
148A LEU* 4.0 25.1 - - + -
149B ARG 5.7 2.0 - - - -
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Residues in contact with VAL 109 (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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87A PRO* 3.5 27.8 - - + -
88A GLN 3.5 6.7 - - - +
89A ALA* 3.8 14.6 - - + +
107A CYS* 4.2 8.7 - - - +
108A PHE* 1.3 75.1 - - - +
110A ASP* 1.3 61.3 + - - +
112A ILE* 3.6 18.8 - - + +
117A ILE* 3.9 0.9 - - + -
119A ILE* 3.3 31.2 - - + -
146A HIS* 3.1 6.3 - - - +
147A LYS 2.9 41.8 + - - +
165A VAL* 3.9 13.9 - - + -
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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