Contacts of the strand formed by residues 131 - 140 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU* 4.8 3.3 - - - +
129A SER 5.0 1.2 + - - -
130A TRP* 1.3 85.1 - - - +
132A CYS* 1.3 63.8 + - - +
157A LEU* 4.2 8.1 - - - -
158A PHE 3.1 13.5 - - - -
159A PHE* 4.1 6.1 - - - -
198A ASP 5.6 0.2 - - - +
199A ALA* 6.2 0.2 - - - -
151B SER 5.7 0.4 - - - -
152B ARG* 3.0 46.3 + - - +
153B ARG 5.0 2.6 + - - -
167B PHE* 4.4 5.9 - - - -
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Residues in contact with CYS 132 (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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93A ARG* 5.9 0.7 - - + -
95A LEU* 3.7 24.7 - - + -
97A TRP* 4.1 20.0 - - + -
130A TRP* 4.7 0.9 - - + -
131A SER* 1.3 76.8 - - - +
133A HIS* 1.3 62.4 + - - +
134A ALA 3.4 2.8 + - - -
156A HIS 3.6 0.2 - - - +
157A LEU* 4.0 1.8 - - - -
158A PHE* 2.8 42.5 + - + +
197A ALA* 4.6 8.1 - - + -
198A ASP* 3.8 8.5 - - - +
152B ARG* 4.0 0.4 - - - +
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Residues in contact with HIS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A CYS* 1.3 71.2 - - - +
134A ALA* 1.3 62.6 + - - +
155A SER* 4.0 20.9 - - - -
156A HIS* 3.5 16.9 + - - -
157A LEU* 3.9 13.0 + - + +
196A GLN 4.0 0.3 - - - +
197A ALA* 3.5 0.5 - - - -
198A ASP* 2.8 52.6 + - + +
150B PHE* 5.8 2.0 - + - -
152B ARG* 3.7 11.5 - - - +
169B ASN* 2.8 46.0 + - - -
170B PHE 4.4 1.1 - - - -
171B MET* 4.3 7.8 - - - -
172B ALA* 4.0 22.3 + - + +
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Residues in contact with ALA 134 (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 TRP* 3.8 29.4 - - + -
119A LEU* 5.7 0.2 - - + -
132A CYS 3.4 0.6 + - - -
133A HIS* 1.3 76.7 + - - +
135A GLN* 1.3 60.3 + - - +
154A ILE* 4.6 0.7 - - - +
155A SER* 3.2 3.6 + - - -
156A HIS 2.8 38.9 + - - +
158A PHE* 4.1 14.0 - - + -
195A VAL* 4.1 7.4 - - + -
196A GLN 3.1 14.6 - - - +
197A ALA* 3.9 4.9 - - + -
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Residues in contact with GLN 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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134A ALA* 1.3 76.2 - - - +
136A ALA* 1.3 62.5 + - - +
153A ARG* 5.2 14.0 + - - +
154A ILE* 3.1 13.7 - - - +
155A SER* 4.3 10.9 + - - +
195A VAL* 3.6 0.5 - - - +
196A GLN* 2.8 64.4 + - + +
112B GLN* 2.6 41.4 + - - +
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Residues in contact with ALA 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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119A LEU* 4.0 14.4 - - + -
134A ALA 5.7 0.2 - - - -
135A GLN* 1.3 75.8 - - - +
137A VAL* 1.3 64.0 + - - +
138A LEU* 4.0 18.1 + - + -
153A ARG* 3.3 7.0 - - - +
154A ILE* 3.0 36.6 + - + +
193A VAL* 4.4 1.6 - - + -
194A PHE* 2.9 17.5 - - - +
195A VAL* 3.8 14.4 - - + -
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Residues in contact with VAL 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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136A ALA* 1.3 76.4 - - - +
138A LEU* 1.3 61.7 + - - +
139A LYS* 3.6 8.5 + - + +
151A SER* 3.8 27.8 - - - +
152A ARG 3.6 6.1 - - - +
153A ARG* 3.6 42.0 - - + +
192A GLU 3.6 1.2 - - - +
193A VAL* 3.3 6.2 - - - -
194A PHE* 2.8 53.7 + - + -
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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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117A PHE* 3.6 54.7 - - + +
119A LEU* 4.4 7.9 - - + +
136A ALA* 4.0 13.2 - - + -
137A VAL* 1.3 76.5 - - - +
139A LYS* 1.3 59.5 + - - +
151A SER* 3.3 1.2 - - - -
152A ARG 2.8 37.2 + - - +
154A ILE* 3.8 28.0 - - + -
165A TRP 4.3 2.9 - - - +
166A GLY* 4.0 16.8 - - - -
167A PHE* 4.4 9.4 - - + -
170A PHE* 3.4 11.1 - - + -
192A GLU 3.7 3.6 - - - -
193A VAL* 4.0 10.5 - - + -
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Residues in contact with LYS 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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117A PHE* 3.5 5.9 - - - -
137A VAL* 3.6 8.9 + - + +
138A LEU* 1.3 75.0 - - - +
140A ILE* 1.3 65.4 + - - +
141A ILE* 3.4 24.3 + - + +
146A ASP* 3.8 16.2 + - - -
149A SER* 3.6 22.2 - - - -
150A PHE 3.4 6.5 - - - +
151A SER* 3.6 17.0 - - - -
191A PHE* 3.5 0.9 - - - -
192A GLU* 2.6 77.3 + - + +
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Residues in contact with ILE 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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115A VAL* 4.4 7.4 - - + -
117A PHE* 4.3 0.4 - - + -
139A LYS* 1.3 71.4 - - - +
141A ILE* 1.3 66.9 + - - +
149A SER* 3.8 0.5 - - - -
150A PHE 2.9 29.0 + - - -
170A PHE* 3.4 24.2 - - + -
171A MET* 3.3 33.9 - - + -
176A VAL* 4.1 10.1 - - + -
183A PHE* 3.7 21.6 - - + -
189A VAL* 3.9 22.7 - - + -
190A THR 3.5 4.7 - - - +
191A PHE* 3.8 34.3 - - + -
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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