Contacts of the strand formed by residues 137 - 142 (chain A) in PDB entry 3SXW
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 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A HIS 3.2 30.1 - - - +
91A PHE* 3.6 27.4 - - + -
99A GLN* 5.1 0.2 - - - +
111A LEU 3.8 0.3 - - - +
112A MET* 3.0 9.0 - - - +
113A GLN* 2.8 32.6 + - + +
136A TRP* 1.3 71.8 - - - +
138A ALA* 1.3 59.2 + - - +
165A ILE* 4.3 2.2 - - + -
170A PHE* 3.8 16.8 - - + -
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 5.6 0.7 - - - +
89A GLY* 3.4 19.4 - - - -
90A HIS* 3.9 9.7 + - - +
99A GLN* 3.8 32.0 - - - +
110A VAL* 3.9 17.5 - - + -
111A LEU 3.6 3.8 - - - -
112A MET* 4.0 1.1 - - + -
132A SER* 3.9 11.9 - - - +
136A TRP 4.2 1.0 + - - -
137A ALA* 1.3 75.0 - - - +
139A ARG* 1.3 60.9 + - - +
140A ALA 4.2 0.4 - - - -
170A PHE* 4.3 1.6 - - - -
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Residues in contact with ARG 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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35A TYR* 3.5 25.1 + - - -
83A GLU* 5.2 1.8 + - - -
86A PHE* 3.7 49.1 - - + -
87A ALA* 3.1 23.5 + - - +
88A LYS 2.8 21.0 + - - -
89A GLY* 4.4 2.0 - - - -
110A VAL* 3.5 2.8 - - - +
111A LEU* 2.8 52.5 + - + +
138A ALA* 1.3 74.7 - - - +
140A ALA* 1.3 60.7 + - - +
141A VAL* 3.6 8.9 + - + +
165A ILE* 3.8 5.1 - - - +
169A GLY* 5.0 2.8 - - - -
170A PHE* 3.4 47.9 - - + +
172A LYS 5.2 1.4 + - - -
173A ILE* 6.0 2.4 - - - +
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Residues in contact with ALA 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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73A HIS* 4.8 10.5 + - + +
75A ILE* 4.0 24.1 - - + +
86A PHE* 3.2 5.0 - - - +
87A ALA* 2.9 33.5 + - + +
109A GLY 3.4 6.3 - - - -
110A VAL* 4.4 4.4 - - + +
138A ALA 4.2 0.4 - - - -
139A ARG* 1.3 71.4 - - - +
141A VAL* 1.3 59.7 + - - +
148A PHE* 4.1 4.0 - - + -
150A MET* 4.1 25.8 - - + -
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Residues in contact with VAL 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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84A PHE* 3.7 22.0 - - + +
85A PHE 3.6 12.6 - - - +
86A PHE* 3.8 15.7 - - + -
108A GLY* 3.1 5.9 - - - -
109A GLY 2.8 33.4 + - - -
111A LEU* 4.5 3.1 - - + -
121A TRP* 3.8 22.8 - - + -
139A ARG* 3.7 18.4 - - + +
140A ALA* 1.3 79.5 - - - +
142A ASN* 1.3 62.0 - - - +
143A ILE* 3.7 11.3 + - + -
148A PHE* 3.4 6.5 - - - -
174A VAL* 4.2 22.0 - - + -
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Residues in contact with ASN 142 (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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75A ILE* 2.8 41.4 + - + +
76A TYR 4.0 4.3 - - - +
77A PRO* 3.3 19.5 - - + +
78A GLY 4.6 2.1 + - - +
84A PHE* 3.2 24.0 - - - +
85A PHE 3.1 11.0 + - - +
107A LYS 3.2 8.1 + - - +
141A VAL* 1.3 69.6 - - - +
143A ILE* 1.3 60.5 + - - +
144A GLY* 2.8 21.7 + - - +
146A GLU 2.7 27.3 + - - +
148A PHE* 3.3 12.7 - - + +
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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