Contacts of the strand formed by residues 137 - 142 (chain C) in PDB entry 2WJZ
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 GLU 137 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ARG* 3.4 4.8 - - - +
134C VAL* 2.7 39.6 + - - +
135C ASP 4.1 7.9 - - - +
136C GLY* 1.3 86.0 - - - +
138C PHE* 1.3 64.1 + - - +
139C MET* 3.4 8.8 + - - +
152C LEU* 3.4 33.8 - - + +
154C ARG* 4.4 8.5 + - - -
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Residues in contact with PHE 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ALA* 5.1 0.7 - - + -
132C LYS 3.5 5.4 - - - -
133C ARG* 3.7 43.3 - - + -
137C GLU* 1.3 71.5 - - - +
139C MET* 1.3 60.9 + - - +
152C LEU* 3.7 8.8 - - - +
153C LEU* 2.9 46.1 + - + -
185C GLU* 4.5 13.0 - - + -
186C MET* 3.6 47.3 - - + -
189C PHE* 3.7 51.0 - + + -
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Residues in contact with MET 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ALA* 3.3 7.0 - - - +
132C LYS 2.9 31.0 + - - +
134C VAL* 3.8 26.5 - - + +
137C GLU* 3.9 9.9 - - - +
138C PHE* 1.3 75.8 - - - +
140C VAL* 1.3 62.7 + - - +
141C PHE* 3.5 20.0 - - + -
148C ASN* 3.9 10.8 - - - +
150C GLY* 3.1 47.8 - - - +
151C ILE 3.3 13.0 - - - +
152C LEU* 3.7 28.7 - - + +
153C LEU* 4.8 0.2 - - - -
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASN* 5.9 0.9 - - - +
107C VAL* 4.2 16.6 - - + -
129C ILE* 4.1 11.2 - - + -
130C ASP 3.8 5.6 - - - +
131C ALA* 4.7 0.2 - - - +
139C MET* 1.3 73.3 - - - +
141C PHE* 1.3 69.9 + - - +
142C THR* 5.0 0.2 - - + -
148C ASN* 3.9 0.7 - - - +
149C THR* 2.8 38.7 + - + +
151C ILE* 2.9 24.7 + - + +
153C LEU* 3.6 32.5 - - + -
156C TRP* 3.8 36.6 - - + -
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Residues in contact with PHE 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASN* 4.2 6.4 - - - +
130C ASP* 2.9 32.8 + - - +
132C LYS* 3.5 41.7 - - + -
134C VAL* 3.7 20.2 - - + -
139C MET* 3.5 28.3 - - + -
140C VAL* 1.3 80.9 - - - +
142C THR* 1.3 63.8 + - - +
145C GLY* 3.5 25.3 + - - -
146C LYS 5.0 2.2 - - - -
147C LYS 3.1 18.2 - - - +
148C ASN* 3.5 26.5 - - + -
173C ILE* 3.8 16.2 - - + -
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Residues in contact with THR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ASN* 4.5 4.9 - - - +
104C THR* 3.7 20.0 - - + -
107C VAL* 3.5 39.7 - - + -
108C GLU* 5.2 1.8 + - + +
140C VAL* 5.0 0.7 - - + -
141C PHE* 1.3 74.6 - - - +
143C TYR* 1.3 86.4 + - - +
144C SER 3.5 2.5 - - - -
145C GLY 3.4 4.4 + - - -
147C LYS* 2.9 35.9 + - - +
149C THR* 3.3 22.9 - - + +
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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