Contacts of the strand formed by residues 123 - 129 (chain A) in PDB entry 2WMH
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 VAL 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LEU* 4.5 3.1 - - + -
84A ILE* 3.2 16.2 - - + +
86A LEU* 3.8 26.0 - - + -
113A LEU* 4.0 26.7 - - + -
116A ALA* 3.6 22.9 - - + -
121A ILE* 3.5 17.0 - - + +
122A PRO* 1.3 79.1 - - - +
124A PHE* 1.3 64.3 + - - +
125A LEU* 4.9 0.4 - - + -
150A VAL 2.9 19.1 + - - +
151A LEU* 3.7 5.7 - - + +
152A LYS* 2.8 33.7 + - - +
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Residues in contact with PHE 124 (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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39A THR* 4.1 10.1 - - - -
41A ILE* 5.2 0.2 - - + -
47A LEU* 4.0 24.9 - - + -
49A LEU* 3.6 17.3 - - + -
83A ALA* 3.7 19.3 - - + -
84A ILE 2.9 8.0 + - - +
85A GLU* 3.4 3.7 - - - -
86A LEU* 2.8 27.5 + - - +
123A VAL* 1.3 76.5 - - - +
125A LEU* 1.3 64.2 + - - +
152A LYS* 3.6 37.9 - - + -
153A GLY* 3.2 24.9 - - - -
154A VAL* 3.8 4.0 - - - -
155A LEU* 3.6 18.3 - - + +
184A HIS* 4.0 14.8 - - + -
186A ILE* 3.8 22.4 - - + -
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Residues in contact with LEU 125 (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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86A LEU* 3.6 36.3 - - + -
109A TYR* 3.8 37.2 - - + +
113A LEU* 4.1 25.6 - - + -
123A VAL* 4.9 0.4 - - + -
124A PHE* 1.3 73.0 - - - +
126A VAL* 1.3 61.5 + - - +
127A ILE* 3.3 15.8 + - + -
140A TRP* 4.3 13.2 - - + -
141A LEU* 5.2 2.9 - - + -
144A GLN* 5.6 0.2 - - + -
151A LEU* 3.7 26.7 - - + -
153A GLY 3.1 7.3 + - - -
154A VAL* 3.1 10.3 - - + +
155A LEU* 2.8 24.2 + - - -
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Residues in contact with VAL 126 (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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85A GLU* 3.4 39.9 - - + +
86A LEU 2.9 17.9 + - - +
87A HIS* 3.8 36.6 - - + +
88A PRO* 3.3 12.6 - - + +
99A PRO* 4.6 2.7 - - + +
109A TYR* 2.8 23.6 + - - -
125A LEU* 1.3 67.9 - - - +
127A ILE* 1.3 54.6 + - - +
128A MET 3.7 20.6 - - - +
129A SER* 4.8 2.5 - - - -
155A LEU* 3.6 11.0 - - + +
157A ILE* 3.8 17.5 - - + -
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Residues in contact with ILE 127 (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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99A PRO* 3.4 12.5 - - - +
109A TYR* 3.5 20.5 + - + +
125A LEU* 3.3 26.4 + - + +
126A VAL* 1.3 76.3 - - - +
128A MET* 1.3 65.5 + - + +
135A THR* 3.4 25.1 - - - +
136A VAL* 4.2 19.0 + - + +
140A TRP* 5.2 2.0 - - + -
141A LEU* 4.1 8.7 - - + -
154A VAL* 3.8 30.3 - - + -
155A LEU 3.0 8.9 + - - +
174A TYR* 3.6 42.6 - - + -
185A PHE* 5.4 0.4 - - + -
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Residues in contact with MET 128 (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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99A PRO* 3.8 4.0 - - - -
126A VAL* 3.7 5.6 - - - +
127A ILE* 1.3 84.1 - - + +
129A SER* 1.3 64.6 + - - +
132A GLU 4.9 5.8 - - - +
135A THR* 4.2 11.0 - - + +
155A LEU 3.3 4.4 + - - +
156A ASN* 3.4 29.5 - - + +
157A ILE 3.0 20.4 + - - -
167A LEU* 3.6 32.8 - - + +
170A HIS* 3.9 14.4 - - + +
171A SER* 3.5 28.0 - - - +
174A TYR* 3.5 37.7 - - + -
185A PHE* 4.2 4.7 - - - -
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Residues in contact with SER 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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97A CYS 3.4 18.6 - - - -
98A ILE* 3.9 0.9 - - - +
99A PRO* 3.7 11.8 - - - +
126A VAL* 4.8 6.5 - - - -
128A MET* 1.3 77.4 - - - +
130A ALA* 1.3 71.3 + - - +
131A GLY 3.1 4.1 + - - -
132A GLU* 3.2 20.1 + - - +
156A ASN* 4.2 3.1 + - - -
157A ILE* 2.7 21.9 + - - -
159A ASN* 3.8 2.2 + - - -
2B FUC 2.8 31.0 + - - +
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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