Contacts of the strand formed by residues 128 - 136 (chain A) in PDB entry 5B82
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 GLY 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A THR* 3.4 5.4 - - - -
125A ASP* 2.9 32.1 + - - +
126A LYS 3.3 0.2 - - - -
127A GLU* 1.3 81.5 - - - +
129A VAL* 1.3 63.6 + - - -
130A HIS* 3.5 6.3 - - - -
179A THR* 5.1 0.4 - - - -
180A ILE 3.5 9.6 - - - -
182A GLN* 3.7 15.0 - - - -
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Residues in contact with VAL 129 (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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26A ALA* 4.1 22.0 - - + -
31A LEU* 4.0 15.7 - - + -
122A TRP* 3.5 36.8 - - + -
123A GLN 3.7 2.7 - - - -
124A THR* 3.8 15.3 - - + -
128A GLY* 1.3 75.7 - - - -
130A HIS* 1.3 63.2 + - - +
131A TYR* 4.3 1.5 + - + +
178A VAL 3.7 0.2 - - - +
179A THR* 3.3 4.3 - - - +
180A ILE* 2.7 50.3 + - + +
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Residues in contact with HIS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.8 18.5 - - + +
121A PHE 3.9 0.5 - - - +
122A TRP* 3.1 5.0 - - - -
123A GLN* 2.9 44.2 + - + +
125A ASP* 2.7 36.3 + - - -
127A GLU* 3.8 20.5 - - + +
128A GLY 3.5 15.0 + - - -
129A VAL* 1.3 72.5 - - - +
131A TYR* 1.3 61.4 + - - +
132A PHE* 3.6 24.3 - - + -
178A VAL 3.1 7.4 - - - +
179A THR* 2.9 32.9 + - + +
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Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.7 29.6 - - + -
35A VAL* 3.8 41.7 + - + +
38A ILE* 4.0 23.1 - - + -
39A GLU* 4.6 4.0 + - - -
120A ALA* 3.4 31.2 - - + +
121A PHE* 3.5 14.6 - - - -
122A TRP* 4.0 21.8 - + + -
129A VAL* 4.3 1.5 - - + -
130A HIS* 1.3 73.3 - - - +
132A PHE* 1.3 62.3 + - - +
133A ARG* 3.8 22.7 - - + +
176A TYR* 3.8 0.8 - - + +
177A ALA* 3.4 3.5 - - - -
178A VAL* 2.8 36.3 + - + +
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Residues in contact with PHE 132 (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* 3.6 40.6 - - + -
105A ASP* 4.3 7.6 - - - -
108A ALA* 3.8 7.2 - - + -
112A PHE* 3.7 21.1 - - + -
120A ALA* 3.1 6.8 - - - +
121A PHE* 2.9 62.1 + + + +
123A GLN* 4.9 1.6 - - + -
130A HIS* 3.6 27.6 - + + -
131A TYR* 1.3 78.3 - - - +
133A ARG* 1.3 60.7 + - - +
175A MET* 3.6 30.3 - - + -
176A TYR 3.2 5.2 - - - +
177A ALA* 3.8 25.1 - - + -
178A VAL 5.4 0.4 - - - -
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Residues in contact with ARG 133 (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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38A ILE* 3.9 21.5 - - + -
39A GLU* 2.8 40.5 + - - +
42A ASP* 4.3 12.7 + - - -
112A PHE* 3.9 3.3 - - - -
119A GLN* 3.1 50.8 + - - +
120A ALA* 3.7 10.1 - - + -
131A TYR* 3.8 15.0 - - + +
132A PHE* 1.3 75.4 - - - +
134A ARG* 1.3 93.3 + - - +
175A MET* 3.2 0.5 - - - -
176A TYR* 2.8 51.8 + - + -
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Residues in contact with ARG 134 (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 ASP* 5.0 1.4 - - - +
112A PHE* 3.0 64.6 + - + +
113A ASP* 4.9 1.4 + - - +
115A ASN 3.0 12.1 + - - -
116A HIS* 3.6 21.1 + - - +
118A LEU 3.0 25.7 + - - -
119A GLN* 2.9 37.1 + - - +
133A ARG* 1.3 102.1 + - - +
135A ILE* 1.3 60.5 + - - +
136A ASP* 2.9 34.8 + - - +
171A ASP 5.8 0.2 - - - -
172A LEU* 4.0 21.9 - - + +
174A GLY 3.8 5.6 - - - -
176A TYR* 4.6 0.3 - - - -
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Residues in contact with ILE 135 (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 ASP* 4.4 9.6 - - - +
45A ARG* 3.8 3.6 - - - +
88A GLN* 4.8 1.1 - - + +
134A ARG* 1.3 73.7 - - - +
136A ASP* 1.3 65.9 + - - +
172A LEU* 3.7 1.4 - - - +
173A ARG* 2.8 35.6 + - + +
174A GLY 2.8 16.4 + - - +
175A MET* 3.5 29.6 - - - +
176A TYR* 3.4 40.2 - - + -
501A HEC 3.5 54.5 - - + -
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Residues in contact with ASP 136 (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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116A HIS 5.2 0.9 - - - +
119A GLN* 4.4 7.4 + - - +
134A ARG* 2.9 44.9 + - - +
135A ILE* 1.3 79.3 - - - +
137A VAL* 1.3 66.1 + - - +
138A GLN* 3.5 21.1 + - - +
170A GLY* 4.6 9.3 - - - +
171A ASP 3.4 12.7 - - - +
172A LEU* 3.9 2.8 - - - +
173A ARG* 4.2 1.3 - - - -
501A HEC 3.4 19.9 - - - +
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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