Contacts of the strand formed by residues 142 - 151 (chain B) in PDB entry 1FBA
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 CYS 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B LEU* 3.7 39.9 - - - -
104B LEU* 3.4 15.7 - - - +
105B GLY 4.4 5.2 - - - -
106B ILE* 3.8 33.0 - - + -
137B TYR* 2.9 18.2 + - + +
138B LYS* 3.3 29.0 + - - +
141B GLY* 1.3 78.1 - - - +
143B ASP* 1.3 60.4 + - - +
144B PHE 3.8 1.3 - - - +
182B ILE* 4.3 4.8 - - + +
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Residues in contact with ASP 143 (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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18B ILE* 3.6 30.4 - - + +
98B LYS* 4.6 8.0 + - - -
103B ILE* 4.0 24.5 - - + +
104B LEU 2.8 7.4 + - - -
138B LYS* 2.8 31.9 + - - +
141B GLY 4.3 7.5 - - - +
142B CYS* 1.3 78.4 - - - +
144B PHE* 1.3 61.6 + - - +
182B ILE* 3.6 8.5 - - - -
183B VAL 3.0 20.1 + - - -
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 4.7 0.2 - - + -
22B ILE* 3.5 28.7 - - + -
29B ILE* 4.3 12.3 - - + -
75B GLY* 4.3 5.6 - - - -
76B VAL 3.9 10.8 - - - -
77B ILE* 3.6 26.2 - - + -
103B ILE* 3.7 22.4 - - + -
104B LEU 3.5 10.7 - - - +
105B GLY* 3.2 27.8 - - - -
106B ILE* 3.2 25.5 + - - +
142B CYS* 4.6 0.3 - - - +
143B ASP* 1.3 78.9 + - - +
145B ALA* 1.3 65.8 + - - +
182B ILE* 3.5 5.4 - - - +
183B VAL* 3.1 19.1 - - + +
185B ILE* 3.5 34.5 - - + -
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Residues in contact with ALA 145 (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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106B ILE* 3.3 13.2 - - + +
108B VAL* 4.3 12.3 - - + -
144B PHE* 1.3 79.2 - - - +
146B LYS* 1.3 60.7 + - - +
173B TYR* 3.3 7.9 - - + +
177B CYS* 3.8 21.1 - - - -
182B ILE* 3.6 17.5 - - + -
183B VAL 2.8 7.1 + - - +
185B ILE* 2.9 32.2 + - - +
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Residues in contact with LYS 146 (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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33B ASP* 2.6 36.6 + - - +
77B ILE* 3.8 31.4 - - + -
106B ILE 3.0 6.3 + - - +
107B LYS* 3.5 22.0 - - + +
108B VAL* 2.9 28.1 + - - +
109B ASP* 3.9 1.3 + - - +
145B ALA* 1.3 75.6 - - - +
147B TRP* 1.3 65.9 + - - +
148B ARG* 4.3 16.4 - - - +
173B TYR* 3.6 3.6 - - - -
185B ILE* 4.3 9.4 - - + +
187B GLU* 3.1 31.8 + - + +
229B LYS* 4.7 11.6 - - + +
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Residues in contact with TRP 147 (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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108B VAL* 4.1 3.8 - - + -
109B ASP* 3.5 25.1 - - + -
124B THR* 3.4 40.9 - - + +
125B GLN 3.4 19.1 - - - -
126B GLY* 3.6 25.4 - - - -
127B LEU* 3.7 26.2 - - + -
130B LEU* 4.4 3.4 - - + -
146B LYS* 1.3 76.7 - - - +
148B ARG* 1.3 66.8 + - - +
149B CYS* 3.6 9.3 - - - -
169B VAL* 3.9 16.4 + - + +
170B LEU* 3.7 19.2 - - + +
173B TYR* 3.4 45.1 + + + +
185B ILE 3.9 2.6 + - - +
187B GLU* 3.2 27.7 + - - +
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Residues in contact with ARG 148 (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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109B ASP* 3.0 16.7 + - - +
112B VAL* 4.7 6.7 - - - +
124B THR* 2.8 30.4 + - - +
146B LYS* 4.3 13.0 - - - +
147B TRP* 1.3 76.6 - - - +
149B CYS* 1.3 62.2 - - - +
150B VAL* 3.6 18.7 - - + +
187B GLU* 3.6 28.5 + - + +
189B GLU* 3.0 34.1 + - - +
191B LEU* 3.8 7.5 - - - +
361B HIS* 2.7 43.9 + - - +
362B ALA 5.4 1.0 - - - +
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Residues in contact with CYS 149 (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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124B THR* 3.5 8.1 - - - -
147B TRP* 3.6 11.4 + - - -
148B ARG* 1.3 73.2 - - - +
150B VAL* 1.3 59.7 + - - +
151B LEU* 5.5 2.0 - - + -
166B ASN* 3.4 27.4 - - + +
169B VAL* 3.6 20.4 - - - -
170B LEU* 3.5 34.5 - - + -
187B GLU 2.9 12.6 + - - +
188B PRO* 4.4 3.4 - - + -
189B GLU* 2.8 33.8 + - - +
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Residues in contact with VAL 150 (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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112B VAL* 4.2 11.5 - - + +
122B VAL* 3.7 23.3 + - + +
124B THR* 4.5 2.2 + - - -
148B ARG* 3.6 39.5 - - + +
149B CYS* 1.3 79.3 - - - +
151B LEU* 1.3 69.9 + - - +
152B LYS* 4.5 2.5 - - + +
162B SER* 4.9 0.3 + - - -
166B ASN* 4.2 3.4 + - - +
189B GLU* 3.5 3.1 - - + +
191B LEU* 3.4 35.0 - - + -
362B ALA* 2.9 37.7 - - + +
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Residues in contact with LEU 151 (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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149B CYS* 5.5 1.6 - - + -
150B VAL* 1.3 75.4 - - - +
152B LYS* 1.3 63.8 + - - +
153B ILE 4.3 0.2 + - - -
158B PRO* 4.3 15.5 - - + -
162B SER* 3.1 36.1 - - - +
163B ILE* 4.6 4.0 - - + +
166B ASN* 3.7 24.5 - - + +
188B PRO* 5.0 7.4 - - + -
189B GLU 2.8 11.8 + - - +
190B VAL* 3.4 13.7 - - + +
191B LEU* 2.8 30.0 + - - +
208B VAL* 3.1 49.4 - - + -
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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