Contacts of the strand formed by residues 102 - 108 (chain A) in PDB entry 1H9D
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 LEU 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A GLY 3.4 16.1 + - - +
101A THR* 1.3 77.1 - - - +
103A VAL* 1.3 64.0 + - - +
104A THR* 5.5 0.7 - - + -
121A THR* 4.2 17.3 - - + -
122A ALA 3.3 11.2 - - - +
123A ALA* 4.1 10.8 - - + -
153A PHE* 2.9 48.6 + - + +
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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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91A VAL* 4.0 16.8 - - + -
101A THR 3.8 9.2 - - - +
102A LEU* 1.3 83.1 - - - +
104A THR* 1.3 66.6 + - - +
121A THR* 3.3 2.8 - - - +
122A ALA 2.6 41.7 + - - +
124A MET* 4.0 11.0 - - + -
129A ALA* 3.7 23.3 - - + -
131A PHE* 3.6 10.1 - - + -
150A ILE* 4.0 17.0 - - + -
151A THR 3.2 10.3 - - - +
152A VAL* 3.9 24.9 - - + -
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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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102A LEU* 5.3 1.1 - - + -
103A VAL* 1.3 79.5 - - - +
105A VAL* 1.3 69.0 + - - +
106A MET* 4.9 5.7 - - - +
120A ALA 3.1 7.4 - - - -
121A THR* 3.9 24.5 - - + +
131A PHE* 4.3 0.9 - - - -
149A THR 3.6 0.5 - - - +
150A ILE* 3.4 6.8 - - - +
151A THR* 3.0 37.9 + - - -
153A PHE* 3.5 30.2 - - + -
65B SER* 4.2 6.8 + - - +
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Residues in contact with VAL 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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89A PHE* 3.8 24.2 - - + -
104A THR* 1.3 80.6 - - - +
106A MET* 1.3 77.6 + - - +
117A LEU* 3.1 24.4 - - + +
120A ALA* 2.9 23.3 + - + +
131A PHE* 3.7 22.0 - - + -
134A LEU* 4.6 13.5 - - + -
136A PHE* 5.1 1.3 - - + -
148A LEU* 4.3 24.9 - - + -
149A THR 3.4 4.9 - - - +
150A ILE* 4.4 9.2 - - + -
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Residues in contact with MET 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 THR* 4.9 7.0 - - - +
105A VAL* 1.3 79.3 - - - +
107A ALA* 1.3 64.5 + - - +
117A LEU* 3.8 6.5 - - - -
148A LEU* 3.4 5.5 - - - +
149A THR* 2.7 37.2 + - + +
151A THR* 4.1 11.9 - - - +
30B THR* 5.1 2.2 - - - -
54B GLU* 4.7 17.9 - - - +
55B ILE 5.6 0.2 - - - +
63B ASN* 3.7 29.2 - - + +
64B LEU* 3.1 13.9 - - - +
65B SER* 2.8 52.3 - - - +
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Residues in contact with ALA 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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106A MET* 1.3 79.8 - - - +
108A GLY* 1.3 58.7 + - - +
114A SER* 3.5 1.0 - - - -
115A ALA* 2.8 36.2 + - + +
117A LEU* 4.3 8.2 - - + +
136A PHE* 4.3 11.0 - - + -
146A PHE* 4.0 15.5 - - + -
147A THR 3.4 5.8 - - - +
148A LEU* 3.6 21.5 - - + -
149A THR* 5.9 0.2 - - - -
63B ASN* 3.4 14.9 + - - +
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Residues in contact with GLY 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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107A ALA* 1.3 77.2 - - - +
109A ASN* 1.3 62.1 + - - +
112A ASN 3.4 11.0 - - - -
113A TYR 3.7 2.0 - - - -
115A ALA 4.4 0.2 - - - -
146A PHE* 3.7 9.8 - - - -
147A THR* 2.8 33.9 + - - +
61B GLY 3.3 18.3 + - - -
63B ASN* 3.7 4.1 - - - +
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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