Contacts of the strand formed by residues 131 - 140 (chain B) in PDB entry 2F1X
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 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B LEU* 4.4 5.7 - - - +
129B SER 5.4 0.4 + - - -
130B TRP* 1.3 83.2 - - - +
132B CYS* 1.3 63.4 + - - +
157B LEU* 4.5 14.8 - - - +
158B PHE 3.3 11.7 - - - -
159B PHE* 4.5 5.2 - - - -
198B ASP* 4.9 2.5 - - - +
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Residues in contact with CYS 132 (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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93B ARG* 6.1 0.4 - - + -
95B LEU* 3.7 22.0 - - + -
97B TRP* 3.9 24.7 - - + -
121B CYS* 4.5 4.9 - - - -
130B TRP* 4.6 0.2 - - + -
131B SER* 1.3 77.3 - - - +
133B HIS* 1.3 59.2 + - - +
157B LEU* 3.4 3.1 - - - -
158B PHE* 2.6 45.9 + - + +
197B ALA* 4.6 7.2 - - + -
198B ASP* 4.0 6.5 - - - +
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Residues in contact with HIS 133 (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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132B CYS* 1.3 71.8 - - - +
134B ALA* 1.3 61.0 + - - +
155B SER* 4.3 17.8 + - - -
156B HIS* 3.6 19.9 + - - -
157B LEU* 3.7 23.3 - - + +
196B GLN 4.1 0.5 - - - +
197B ALA* 3.6 0.2 - - - -
198B ASP* 3.0 53.3 + - + +
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Residues in contact with ALA 134 (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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97B TRP* 3.6 30.3 - - + -
119B LEU* 5.7 0.2 - - + -
132B CYS 3.6 0.6 + - - -
133B HIS* 1.3 76.9 + - - +
135B GLN* 1.3 60.3 + - - +
136B ALA* 5.5 0.4 - - + -
154B ILE* 4.6 0.7 - - - +
155B SER* 3.3 4.0 + - - -
156B HIS 2.8 38.4 + - - +
158B PHE* 3.9 10.6 - - + -
195B VAL* 3.9 10.3 - - + -
196B GLN 3.2 13.5 - - - +
197B ALA* 3.9 4.9 - - - -
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Residues in contact with GLN 135 (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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134B ALA* 1.3 74.5 - - - +
136B ALA* 1.3 67.0 + - - +
153B ARG* 5.8 7.8 - - + -
154B ILE* 3.4 12.6 - - - +
155B SER* 4.2 10.5 - - - +
195B VAL* 3.5 0.9 - - - +
196B GLN* 2.9 60.9 + - - +
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Residues in contact with ALA 136 (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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119B LEU* 3.8 24.0 - - + -
134B ALA 5.5 0.4 - - - -
135B GLN* 1.3 80.3 - - - +
137B VAL* 1.3 64.7 + - - +
138B LEU* 4.1 5.4 - - + -
153B ARG* 3.3 5.6 - - - +
154B ILE* 2.8 50.8 + - + +
158B PHE* 6.2 0.2 - - + -
193B VAL* 4.5 1.1 - - + -
194B PHE* 3.0 13.7 - - - +
195B VAL* 3.8 9.2 - - + -
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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
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136B ALA* 1.3 74.9 - - - +
138B LEU* 1.3 63.7 + - - +
139B LYS* 3.9 8.0 + - + +
151B SER* 3.9 20.4 - - - -
152B ARG 3.6 4.7 - - - +
153B ARG* 3.6 40.4 - - - +
192B GLU 3.6 1.6 - - - +
193B VAL* 3.4 7.1 - - - -
194B PHE* 2.8 56.4 + - + +
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Residues in contact with LEU 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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117B PHE* 3.3 56.1 - - + +
118B PHE* 4.4 4.3 - - - -
119B LEU* 4.6 5.8 - - + +
136B ALA* 4.1 8.1 - - + -
137B VAL* 1.3 77.7 - - - +
139B LYS* 1.3 60.2 + - - +
151B SER* 3.1 1.8 - - - -
152B ARG 2.8 41.4 + - - +
154B ILE* 3.8 31.0 - - + -
165B TRP 4.7 0.2 - - - +
166B GLY* 4.2 15.7 - - - -
167B PHE* 4.2 10.8 - - + -
170B PHE* 3.4 8.9 - - + -
192B GLU 3.7 3.6 - - - -
193B VAL* 4.3 9.6 - - + -
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Residues in contact with LYS 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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117B PHE* 3.5 3.8 - - - -
137B VAL* 3.9 7.6 + - + +
138B LEU* 1.3 75.2 - - - +
140B ILE* 1.3 62.0 + - - +
141B ILE* 4.0 15.6 - - + +
146B ASP* 3.4 27.3 + - - -
149B SER* 3.9 14.6 + - - -
150B PHE 3.1 6.5 - - - +
151B SER* 3.5 23.3 - - - -
170B PHE* 4.3 0.2 - - - -
191B PHE* 3.6 2.3 - - - -
192B GLU* 2.7 81.6 + - + +
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Residues in contact with ILE 140 (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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115B VAL* 4.2 9.9 - - + -
117B PHE* 4.1 0.7 - - + -
139B LYS* 1.3 73.2 - - - +
141B ILE* 1.3 65.6 + - - +
142B ASN 3.6 0.3 + - - -
149B SER* 3.7 1.3 - - - -
150B PHE 3.0 27.2 + - - +
170B PHE* 3.5 20.2 - - + -
171B MET* 3.2 31.0 - - + -
176B VAL* 4.2 9.6 - - + -
183B PHE* 3.7 19.6 - - + -
189B VAL* 3.6 25.6 - - + -
190B THR 3.6 4.0 - - - +
191B PHE* 3.4 39.0 - - + -
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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