Contacts of the strand formed by residues 136 - 141 (chain A) in PDB entry 6ABP
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 ALA 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A SER* 1.3 77.0 - - - +
137A VAL* 1.3 61.8 + - - +
164A PHE* 3.8 3.6 - - - -
168A GLN* 3.4 16.6 - - + +
170A TYR* 3.5 22.2 - - + -
196A VAL* 3.6 19.5 - - + -
198A HIS 3.0 6.9 + - - -
199A TRP* 3.5 15.2 - - + -
200A LEU* 3.0 27.9 + - - +
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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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136A ALA* 1.3 73.6 - - - +
138A MET* 1.3 67.0 - - - +
139A ALA* 4.2 2.9 - - + +
156A MET* 4.9 1.1 - - + -
159A LEU* 3.9 16.2 - - + -
164A PHE* 3.7 24.2 - - + -
168A GLN 3.1 4.5 + - - +
169A ILE* 4.0 27.4 - - + -
170A TYR* 2.9 26.5 + - - -
199A TRP* 3.8 7.2 - - - -
200A LEU* 3.3 28.9 - - + +
202A VAL* 3.8 27.8 - - + -
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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
----------------------------------------------------------
137A VAL* 1.3 73.9 - - - +
139A ALA* 1.3 54.2 - - - +
140A ILE* 4.0 13.6 + - + -
170A TYR* 3.5 3.4 - - - +
172A VAL* 4.3 9.4 - - + -
186A ALA* 3.5 45.1 - - + +
189A MET* 4.3 14.8 - - + -
190A LEU* 4.9 7.2 - - + -
199A TRP* 3.7 18.7 - - + -
200A LEU 2.7 11.7 + - - +
201A ILE* 3.4 37.7 - - + +
202A VAL 2.8 31.2 + - - +
212A GLY* 4.5 0.4 - - - -
216A THR* 4.5 10.1 - - + -
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Residues in contact with ALA 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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137A VAL* 3.8 3.8 - - + -
138A MET* 1.3 73.4 - - - +
140A ILE* 1.4 61.5 + - - +
141A THR* 3.6 7.5 + - + +
152A THR* 5.4 0.9 - - - -
156A MET* 3.6 36.6 - - + -
169A ILE* 4.9 0.2 - - + -
170A TYR 2.6 16.6 + - - +
171A GLN* 3.3 7.9 - - + -
172A VAL* 2.8 29.8 + - - +
202A VAL* 3.6 15.0 - - + -
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Residues in contact with ILE 140 (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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138A MET* 4.1 15.9 - - + +
139A ALA* 1.4 71.6 - - - +
141A THR* 1.3 60.3 + - - +
142A ALA 4.3 0.2 + - - -
152A THR* 3.7 15.4 - - - +
172A VAL* 3.3 12.8 - - + +
174A THR* 3.5 30.5 - - - -
182A ALA* 4.1 13.9 - - - +
185A ALA* 4.2 9.0 - - + -
186A ALA* 4.2 4.9 - - + -
201A ILE* 4.1 13.9 - - + -
202A VAL* 2.8 13.2 + - - +
203A GLY* 3.8 7.4 - - - -
204A MET* 4.5 1.6 + - - +
208A THR* 3.6 34.1 - - + +
209A VAL* 5.3 0.2 - - - -
212A GLY* 3.7 29.8 - - - -
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Residues in contact with THR 141 (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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139A ALA* 3.8 20.9 - - + +
140A ILE* 1.3 78.4 - - - +
142A ALA* 1.3 60.8 + - - +
143A ASN* 3.6 24.7 + - - +
144A GLU* 5.3 0.5 - - - +
152A THR* 4.1 18.8 - - - +
156A MET* 4.9 2.7 - - + -
171A GLN* 3.9 23.9 + - + +
172A VAL 2.8 18.2 + - - -
173A PRO* 3.4 13.0 - - - +
174A THR* 2.8 33.9 + - - +
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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