Contacts of the strand formed by residues 131 - 139 (chain A) in PDB entry 3KGA
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 ARG 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLN* 4.0 29.8 - - - +
127A LEU* 3.2 6.4 - - - +
128A TYR 2.9 32.8 + - - +
129A ALA 3.3 3.6 - - - +
130A GLY* 1.3 79.6 - - - +
132A LYS* 1.3 64.1 + - - +
133A CYS* 3.5 6.4 - - - -
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Residues in contact with LYS 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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96A GLN* 3.5 5.0 - - - +
97A ASP* 2.8 50.6 + - + +
102A ARG* 4.4 2.8 - - - +
125A GLU* 3.6 30.7 + - + -
126A ASN 3.8 6.7 - - - +
127A LEU* 3.3 15.4 - - + +
131A ARG* 1.3 73.7 - - - +
133A CYS* 1.3 65.3 + - - +
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Residues in contact with CYS 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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94A MET* 5.0 9.0 - - - -
95A LEU 3.3 13.5 - - - +
96A GLN* 4.3 9.6 - - - -
97A ASP* 4.0 2.9 - - - +
124A TYR 3.3 1.0 - - - +
125A GLU* 3.2 9.9 - - - +
126A ASN 2.8 38.4 + - - +
128A TYR* 4.0 17.0 - - + -
131A ARG* 3.5 18.4 - - - -
132A LYS* 1.3 81.2 - - - +
134A LEU* 1.3 64.7 + - - +
135A LEU* 3.5 24.1 + - + +
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Residues in contact with LEU 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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54A ILE* 4.5 10.3 - - + -
93A LYS 3.5 3.8 - - - +
95A LEU* 2.8 41.1 + - + +
97A ASP* 3.9 20.6 - - + +
101A ALA* 3.8 35.4 - - + +
102A ARG* 3.9 35.9 - - - +
105A VAL* 3.9 22.4 - - + -
123A VAL* 4.6 5.4 - - + -
124A TYR 3.3 7.0 - - - +
125A GLU* 4.3 9.4 - - + -
133A CYS* 1.3 77.4 - - - +
135A LEU* 1.3 62.9 + - - +
136A ILE* 4.0 1.8 + - + +
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Residues in contact with LEU 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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59A ILE* 4.1 15.9 - - + -
92A LEU* 3.8 22.9 - - + -
93A LYS 3.6 2.5 - - - -
94A MET* 4.0 26.2 - - + -
122A ASP 3.9 0.5 - - - +
123A VAL* 3.3 3.7 - - - -
124A TYR* 2.7 49.8 + - + +
126A ASN* 3.6 39.9 - - + +
128A TYR* 4.5 13.7 - - + -
133A CYS* 3.5 20.4 - - + -
134A LEU* 1.3 80.6 - - - +
136A ILE* 1.3 60.5 + - - +
137A VAL 3.9 0.3 + - - -
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Residues in contact with ILE 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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91A ALA 3.5 0.5 - - - +
92A LEU* 3.3 7.8 - - - +
93A LYS* 2.9 52.4 + - + +
95A LEU* 4.1 17.7 - - + -
104A GLU* 4.7 4.0 - - + +
105A VAL* 3.4 33.4 - - + -
108A HIS* 5.7 2.0 - - + +
120A ILE* 3.9 32.8 - - + -
122A ASP 3.7 2.0 - - - -
123A VAL* 4.2 9.4 - - + +
134A LEU 4.4 5.2 - - - +
135A LEU* 1.3 75.5 - - - +
137A VAL* 1.3 63.0 + - - +
138A MET* 3.6 27.8 + - + +
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Residues in contact with VAL 137 (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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59A ILE* 3.8 28.5 - - + -
63A TYR* 3.8 27.1 - - + +
81A ILE* 4.2 4.3 - - + -
90A PHE* 3.8 27.8 - - + -
91A ALA 3.4 4.9 - - - +
92A LEU* 4.0 4.0 - - + -
120A ILE* 3.7 5.0 - - - +
121A VAL* 2.7 36.8 + - + -
122A ASP 2.8 25.1 + - - +
124A TYR* 3.9 14.4 - - + -
136A ILE* 1.3 73.4 - - - +
138A MET* 1.3 58.3 + - - +
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Residues in contact with MET 138 (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 PHE* 3.4 12.3 - - - -
91A ALA* 2.8 34.4 + - + +
92A LEU 5.9 0.2 - - - -
93A LYS* 4.3 24.2 - - + -
104A GLU* 5.6 0.4 - - - +
108A HIS* 3.5 29.2 - - + +
118A VAL* 4.3 13.5 - - + -
119A ARG 3.4 13.5 - - - +
120A ILE* 4.5 3.6 - - + -
121A VAL* 4.3 0.9 - - - +
136A ILE* 3.7 30.3 - - + +
137A VAL* 1.3 78.9 - - - +
139A GLU* 1.3 73.8 + - - +
140A CYS 3.4 0.7 + - - -
365A LX9 3.9 35.0 - - + +
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Residues in contact with GLU 139 (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 PHE* 4.2 10.5 - - + -
118A VAL* 3.6 15.3 - - + +
119A ARG* 2.9 55.3 + - + +
121A VAL* 4.2 3.4 - - - +
138A MET* 1.3 71.3 - - - +
140A CYS* 1.3 61.4 + - - +
141A LEU* 4.3 8.6 - - + +
195A THR* 4.2 8.5 - - - +
204A LYS* 3.1 35.6 + - - -
365A LX9 2.9 23.9 + - - -
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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