Contacts of the strand formed by residues 134 - 142 (chain A) in PDB entry 4WMB
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A VAL* 3.2 12.6 - - + +
98A TYR* 2.8 37.0 + - + -
130A PHE* 3.5 19.2 - - + +
131A GLU* 2.9 31.2 + - - +
132A ALA 4.1 2.8 - - - +
133A HIS* 1.3 107.4 + - + +
135A VAL* 1.3 62.0 + - - +
165A LYS* 3.8 19.8 + - - +
235A ARG* 2.3 35.1 + - - -
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Residues in contact with VAL 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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95A PRO* 5.0 8.1 - - + -
96A VAL 2.9 13.3 + - - +
97A ASP* 2.8 26.5 - - - +
98A TYR* 2.8 36.0 + - - +
130A PHE* 5.6 0.7 - - - -
133A HIS 4.8 3.8 - - - +
134A GLU* 1.3 76.3 - - - +
136A LEU* 1.3 62.7 + - - +
137A ASN* 3.4 21.4 + - - +
165A LYS* 3.5 30.3 - - + +
167A LYS* 4.2 13.9 - - + +
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Residues in contact with LEU 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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98A TYR* 3.6 12.3 - - + +
100A LEU* 3.8 32.3 - - + -
124A LEU* 5.1 2.9 - - + -
125A LEU* 4.4 9.6 - - + -
128A ALA* 5.0 1.8 - - + -
130A PHE* 3.9 30.8 - - + -
135A VAL* 1.3 70.7 - - - +
137A ASN* 1.3 61.4 + - - +
138A LEU* 3.6 21.8 - - + -
164A PHE* 3.9 33.8 - - + -
165A LYS 3.0 7.6 + - - +
166A CYS* 3.4 14.5 - - - -
167A LYS 2.9 23.8 + - - -
234A ILE* 4.8 6.7 - - + -
238A PHE* 5.2 0.7 - - + -
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Residues in contact with ASN 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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97A ASP* 2.8 35.7 + - - +
98A TYR 2.6 21.0 + - - +
99A HIS* 3.4 24.7 + - + -
100A LEU* 2.9 32.9 + - - +
135A VAL* 3.4 11.6 + - - +
136A LEU* 1.3 71.8 - - - +
138A LEU* 1.3 62.2 + - - +
139A HIS* 3.8 6.3 - - + -
167A LYS* 3.4 30.6 - - - +
169A ILE* 3.8 7.2 - - + +
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Residues in contact with LEU 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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100A LEU* 3.9 23.8 - - + -
102A MET* 4.9 4.3 - - + -
121A LEU* 5.0 8.1 - - + -
124A LEU* 4.4 7.9 - - + -
125A LEU* 4.3 17.9 - - + -
136A LEU* 3.6 26.9 - - + -
137A ASN* 1.3 70.9 - - - +
139A HIS* 1.3 63.2 + - - +
140A PHE* 3.6 29.6 - - + -
154A LEU* 5.5 3.4 - - + -
158A LEU* 5.1 3.6 - - + -
166A CYS* 3.6 28.0 - - - -
167A LYS 2.8 11.6 + - - +
168A VAL* 3.5 9.9 - - + -
169A ILE* 2.8 27.3 + - - +
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Residues in contact with HIS 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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99A HIS* 2.9 42.2 - + + +
100A LEU 2.8 28.3 + - - +
101A LEU* 3.3 14.7 - - + -
102A MET* 2.9 26.9 + - - +
137A ASN* 3.7 12.9 + - + -
138A LEU* 1.3 72.5 - - - +
140A PHE* 1.3 64.3 + - - +
141A VAL 4.3 0.2 - - - -
169A ILE* 3.3 21.7 - - + +
171A HIS* 2.9 36.1 - + + -
214A MET* 4.4 6.3 - - - -
218A ILE* 3.8 13.1 - - + +
221A ILE* 3.9 10.2 - - + +
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Residues in contact with PHE 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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102A MET* 3.4 33.7 - - + -
104A PHE* 4.4 14.4 - + + -
121A LEU* 3.9 29.2 - - + -
138A LEU* 3.6 35.7 - - + -
139A HIS* 1.3 76.5 - - - +
141A VAL* 1.3 57.7 + - - +
142A SER* 3.8 7.9 + - - +
150A ALA* 5.0 4.5 - - + -
154A LEU* 3.8 27.6 - - + -
168A VAL* 4.0 6.7 - - + -
169A ILE 2.7 10.0 + - - -
170A PHE* 3.3 35.1 - + + -
171A HIS* 2.8 33.4 + - - +
226A LEU* 4.9 4.0 - - + -
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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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101A LEU* 3.9 32.1 - - + -
102A MET 3.0 6.0 + - - +
103A MET* 3.7 22.2 - - + -
104A PHE 2.7 31.5 + - - +
105A THR* 3.4 4.8 - - - +
140A PHE* 1.3 72.7 - - - +
142A SER* 1.3 62.3 + - - +
171A HIS* 3.4 8.1 - - + +
173A VAL* 4.0 22.0 - - + -
176A LEU* 3.9 31.9 - - + -
203A ILE* 4.0 8.1 - - + -
206A LEU* 4.0 6.3 - - + -
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Residues in contact with SER 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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104A PHE* 2.7 34.6 + - - +
105A THR* 4.0 2.9 - - - -
140A PHE* 3.9 11.3 - - - +
141A VAL* 1.3 76.1 + - - +
143A GLU* 1.3 71.0 + - - +
146A SER* 4.0 0.2 - - - -
147A ARG* 3.8 20.3 + - - +
170A PHE* 4.2 8.7 - - - +
171A HIS 3.1 16.5 + - - +
172A ASP* 3.7 5.0 - - - +
173A VAL* 3.4 12.8 + - - -
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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