Contacts of the strand formed by residues 114 - 121 (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 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PRO* 3.5 4.9 - - - +
104B ARG* 2.9 35.5 + - - +
106B TYR* 2.6 42.6 + - - -
112B GLN 3.5 0.6 + - - -
113B LYS* 1.3 75.8 - - - +
115B VAL* 1.3 62.2 + - - +
168B SER 2.9 15.3 + - - -
169B ASN* 3.5 11.7 - - - -
171B MET 3.5 7.0 - - - -
172B ALA* 5.1 0.9 - - - -
173B TRP* 3.7 5.8 - - - -
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 4.2 10.3 - - + -
101B VAL* 4.5 3.1 - - + -
102B MET 4.1 1.1 - - - -
114B SER* 1.3 72.3 - - - +
116B GLY* 1.3 66.2 + - - +
117B PHE* 4.7 2.7 - - + +
140B ILE* 4.2 7.4 - - + -
168B SER 3.4 3.8 - - - +
170B PHE* 3.0 29.9 + - + +
171B MET* 2.9 25.9 + - + +
172B ALA 4.3 0.7 - - - +
173B TRP* 3.6 17.7 - - + -
176B VAL* 3.6 34.3 - - + -
191B PHE* 4.0 28.3 - - + -
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Residues in contact with GLY 116 (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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100B MET 3.4 0.5 - - - +
101B VAL* 3.1 12.3 - - - +
102B MET 2.6 41.2 + - - -
104B ARG* 3.9 5.1 - - - +
114B SER 3.7 0.8 + - - -
115B VAL* 1.3 73.6 - - - +
117B PHE* 1.3 58.7 + - - -
118B PHE* 3.9 17.2 - - - -
167B PHE 3.6 7.4 - - - -
168B SER 3.9 7.9 - - - -
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Residues in contact with PHE 117 (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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99B ILE* 3.4 25.4 - - + -
100B MET 3.5 7.0 - - - -
101B VAL* 4.9 0.2 - - - +
115B VAL* 3.7 1.7 + - + -
116B GLY* 1.3 71.9 - - - +
118B PHE* 1.3 66.7 + - - +
138B LEU* 3.3 23.8 - - + +
139B LYS 3.5 32.8 - - - -
167B PHE 3.0 31.4 + - - -
170B PHE* 3.8 40.4 - + + -
191B PHE* 3.7 35.2 - + + -
192B GLU 3.6 18.2 - - - -
193B VAL* 4.0 12.1 - - + -
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLY 3.5 18.4 - - - -
202A GLY 3.6 11.4 - - - -
203A SER* 3.6 24.2 - - - -
99B ILE* 3.6 3.3 - - - -
100B MET* 2.7 55.6 + - + +
102B MET* 3.6 28.9 - - - -
104B ARG* 4.3 2.7 - - - -
116B GLY* 3.9 17.3 - - - -
117B PHE* 1.3 82.0 - - - +
119B LEU* 1.3 62.7 + - - +
138B LEU* 4.4 2.2 - - - -
164B ASP* 4.3 4.3 - - - -
165B TRP 3.5 8.3 - - - +
166B GLY* 3.5 22.2 - - - -
168B SER* 3.4 37.9 - - - -
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Residues in contact with LEU 119 (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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71B PHE* 4.3 8.5 - - + -
97B TRP* 3.8 37.9 - - + -
98B LYS 3.5 18.2 - - - +
99B ILE* 5.0 0.2 - - - +
118B PHE* 1.3 73.2 - - - +
120B GLN* 1.3 60.7 + - - +
136B ALA* 3.8 28.3 - - + -
138B LEU* 4.6 8.2 - - + +
154B ILE* 4.1 9.2 - - + -
158B PHE* 3.5 15.1 - - + -
164B ASP* 3.0 4.5 - - - -
165B TRP 2.7 38.6 + - - +
193B VAL* 4.0 23.6 - - + -
195B VAL* 4.0 8.5 - - + -
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Residues in contact with GLN 120 (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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86B LEU* 3.7 22.0 - - + +
96B PRO 3.9 0.3 - - - +
97B TRP* 3.3 9.6 - - - +
98B LYS* 2.8 72.5 + - + +
100B MET* 3.4 27.0 - - + +
118B PHE 4.0 0.2 + - - -
119B LEU* 1.3 74.2 - - - +
121B CYS* 1.3 66.4 + - - +
122B ASN 5.8 0.4 - - - +
123B ALA* 3.5 33.2 - - + +
163B ASN* 3.3 15.1 + - - +
164B ASP* 3.8 8.1 - - + -
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Residues in contact with CYS 121 (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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95B LEU* 3.9 17.7 - - - -
96B PRO 3.6 2.9 - - - -
97B TRP* 3.7 46.0 - - + -
120B GLN* 1.3 77.3 - - - +
122B ASN* 1.3 71.9 + - - +
123B ALA 3.0 3.2 + - - -
130B TRP* 3.1 36.5 - - - -
132B CYS* 4.5 0.2 - - - -
158B PHE* 3.8 15.7 - - + -
163B ASN* 2.5 18.4 + - - +
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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