Contacts of the strand formed by residues 134 - 139 (chain B) in PDB entry 4GWF
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 SER 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 3.4 13.5 - - - +
130B GLY* 3.5 13.9 - - - -
131B LYS* 2.8 35.9 + - - +
132B HIS 3.5 0.2 - - - -
133B GLY* 1.4 76.1 - - - +
135B PHE* 1.3 57.5 + - - +
151B VAL* 3.5 0.7 - - - -
152B ARG 2.7 31.9 + - - -
214B GLN* 3.2 24.0 + - - +
215B PRO 5.0 3.1 + - - -
216B LEU* 4.6 4.9 - - - -
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Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TRP* 3.5 37.3 - + + +
126B LEU* 4.2 2.4 - - - +
133B GLY 3.6 8.7 - - - -
134B SER* 1.3 74.8 - - - +
136B LEU* 1.3 66.3 + - - +
137B VAL* 5.1 0.2 - - + -
149B LEU* 3.9 18.6 - - + -
150B SER 3.3 10.3 - - - +
151B VAL* 3.8 16.4 - - + -
194B VAL* 3.6 25.8 - - + -
198B LYS* 4.2 12.6 - - - -
212B LEU* 3.6 35.7 - - + -
214B GLN* 3.2 31.3 + - - -
215B PRO* 3.5 7.6 - - + +
216B LEU* 3.3 22.9 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TRP 3.3 13.7 - - - +
114B HIS* 3.7 13.0 - - + +
117B LEU* 4.2 16.6 - - + -
122B ALA* 4.0 27.4 - - + +
126B LEU* 3.8 28.3 - - + -
135B PHE* 1.3 77.4 - - - +
137B VAL* 1.3 66.5 + - - +
138B ARG* 4.1 20.0 - - + -
149B LEU* 3.4 6.7 - - - +
150B SER* 2.9 46.1 + - - +
216B LEU* 4.1 19.1 - - + -
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TRP* 2.8 35.4 + - + +
113B PHE* 3.6 15.3 - - + -
114B HIS* 3.0 26.7 + - - +
115B GLY 3.5 1.2 + - - -
135B PHE* 5.1 1.1 - - + -
136B LEU* 1.3 78.1 - - - +
138B ARG* 1.3 62.3 + - - +
147B PHE* 4.0 23.6 - - + -
148B VAL 3.4 5.4 - - - +
149B LEU* 3.8 19.7 - - + -
172B ILE* 4.4 8.1 - - + -
190B LEU* 4.1 17.3 - - + -
194B VAL* 3.9 13.9 - - + -
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B HIS* 4.9 0.2 - - + -
115B GLY* 3.7 9.9 - - - +
117B LEU* 3.5 28.9 + - + +
118B SER* 3.9 2.4 - - - +
119B GLY* 3.5 32.5 - - - +
122B ALA* 3.6 24.7 - - - +
136B LEU* 4.1 9.6 - - + -
137B VAL* 1.3 73.2 - - - +
139B GLU* 1.3 68.6 + - - +
140B SER* 5.1 2.2 - - - +
141B GLN* 5.3 3.6 - - - +
147B PHE* 3.3 9.8 - - - +
148B VAL* 2.8 67.5 + - + +
150B SER* 3.4 12.3 + - - -
169B HIS* 3.3 28.7 + - - +
171B MET* 5.7 1.6 - - - +
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PHE* 3.8 10.7 - - - -
115B GLY* 2.8 38.6 + - - +
116B HIS* 4.0 7.3 + - - -
117B LEU 3.9 12.6 - - - +
138B ARG* 1.3 78.1 + - - +
140B SER* 1.3 67.0 + - - +
141B GLN* 3.6 6.9 + - - +
146B ASP 3.9 1.8 - - - +
147B PHE* 3.6 26.7 - - + -
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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