Contacts of the strand formed by residues 142 - 151 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LEU* 5.4 0.2 - - - -
83A LEU* 3.8 39.3 - - - -
104A LEU* 3.4 12.3 - - - +
105A GLY 4.4 8.1 - - - -
106A ILE* 3.8 33.4 - - + -
137A TYR* 3.0 18.5 + - + +
138A LYS* 3.3 27.9 - - - +
141A GLY* 1.3 78.5 - - - +
143A ASP* 1.3 62.0 + - - +
144A PHE 3.8 1.8 - - - +
182A ILE* 3.4 4.8 - - + +
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Residues in contact with ASP 143 (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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18A ILE* 3.7 29.0 - - + +
98A LYS* 4.9 6.9 + - - -
103A ILE* 3.9 25.2 - - + +
104A LEU 2.9 7.1 + - - -
138A LYS* 2.7 33.0 + - - +
141A GLY 4.2 9.4 - - - +
142A CYS* 1.3 75.9 - - - +
144A PHE* 1.3 62.1 + - - +
182A ILE* 3.7 9.6 - - - -
183A VAL 3.0 19.4 + - - -
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Residues in contact with PHE 144 (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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22A ILE* 3.6 28.9 - - + -
29A ILE* 4.2 13.0 - - + -
75A GLY* 4.3 6.1 - - - -
76A VAL 3.8 17.9 - - - -
77A ILE* 3.7 19.5 - - + -
103A ILE* 3.7 22.2 - - + -
104A LEU 3.5 10.5 - - - +
105A GLY* 3.2 28.5 - - - -
106A ILE* 3.1 26.2 + - - +
143A ASP* 1.3 79.2 + - - +
145A ALA* 1.3 64.3 + - - +
182A ILE* 3.6 6.3 - - - +
183A VAL* 3.0 17.9 - - + +
185A ILE* 3.5 32.5 - - + -
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Residues in contact with ALA 145 (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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106A ILE* 3.2 14.4 - - + +
108A VAL* 4.2 15.9 - - + -
134A CYS* 5.5 0.9 - - - -
144A PHE* 1.3 78.9 - - - +
146A LYS* 1.3 60.4 + - - +
173A TYR* 3.3 4.9 - - - +
177A CYS* 3.8 19.7 - - - -
182A ILE* 3.7 16.4 - - + -
183A VAL 2.8 7.0 + - - +
185A ILE* 2.9 32.7 + - - +
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Residues in contact with LYS 146 (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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33A ASP* 2.6 37.8 + - - +
77A ILE* 4.0 31.9 - - + -
106A ILE 3.0 5.3 + - - -
107A LYS* 3.5 23.4 - - + +
108A VAL* 2.9 28.6 + - - +
109A ASP* 3.8 1.8 + - - +
145A ALA* 1.3 76.5 - - - +
147A TRP* 1.3 64.0 + - - +
148A ARG* 4.1 22.1 - - - +
173A TYR* 3.6 2.9 - - - -
185A ILE* 4.3 9.0 - - + +
187A GLU* 3.3 28.2 + - - +
229A LYS* 5.1 9.1 - - + +
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Residues in contact with TRP 147 (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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108A VAL* 4.2 3.8 - - + -
109A ASP* 3.4 24.9 - - + -
124A THR* 3.3 43.0 - - + +
125A GLN 3.6 13.5 - - - -
126A GLY* 3.6 33.0 - - - -
127A LEU* 3.6 22.9 - - + -
130A LEU* 4.4 4.9 - - + -
146A LYS* 1.3 77.4 - - - +
148A ARG* 1.3 64.5 + - - +
149A CYS* 3.6 12.7 - - - -
169A VAL* 3.9 16.0 - - + +
170A LEU* 3.7 18.4 - - + +
173A TYR* 3.4 45.1 + + + +
185A ILE 4.0 2.3 + - - +
187A GLU* 3.3 27.0 + - - +
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Residues in contact with ARG 148 (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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109A ASP* 3.0 15.9 + - - +
112A VAL* 4.6 6.7 - - + +
124A THR* 2.8 28.1 + - - +
146A LYS* 4.1 15.2 - - - +
147A TRP* 1.3 77.0 - - - +
149A CYS* 1.3 64.4 + - - +
150A VAL* 3.5 17.8 - - + +
187A GLU* 3.6 28.4 + - + +
189A GLU* 2.9 31.9 + - - +
191A LEU* 3.7 4.4 - - - +
361A HIS* 2.5 56.8 + - - +
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Residues in contact with CYS 149 (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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124A THR* 3.6 7.6 - - - -
147A TRP* 3.6 19.5 + - - -
148A ARG* 1.3 74.8 - - - +
150A VAL* 1.3 63.5 + - - +
151A LEU* 5.4 2.0 - - + -
166A ASN* 3.4 27.6 - - + +
169A VAL* 3.7 13.0 - - - -
170A LEU* 3.6 33.2 - - + -
187A GLU 2.9 13.4 + - - +
188A PRO* 4.5 4.3 - - + -
189A GLU* 2.9 30.5 + - - +
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Residues in contact with VAL 150 (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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112A VAL* 4.2 15.7 - - + -
122A VAL* 3.7 26.0 + - + +
124A THR* 4.6 1.8 + - - -
148A ARG* 3.5 37.9 - - + +
149A CYS* 1.3 79.7 - - - +
151A LEU* 1.3 67.5 + - - +
152A LYS* 5.5 0.9 - - - -
162A SER* 5.0 0.3 + - - -
166A ASN* 4.3 3.0 + - - -
189A GLU* 3.5 2.5 - - - +
191A LEU* 3.2 44.4 - - + -
361A HIS* 4.2 2.9 - - + +
362A ALA* 3.6 23.7 - - + +
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Residues in contact with LEU 151 (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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149A CYS* 5.4 2.0 - - + -
150A VAL* 1.3 75.5 - - - +
152A LYS* 1.3 61.5 + - - +
158A PRO* 4.3 19.1 - - + -
162A SER* 3.2 35.7 - - - +
163A ILE* 4.7 3.8 - - + +
166A ASN* 3.8 24.2 - - + +
188A PRO* 4.7 11.2 - - + -
189A GLU 2.8 10.6 + - - +
190A VAL* 3.5 13.3 - - + -
191A LEU* 2.9 32.4 + - - +
208A VAL* 3.2 44.4 - - + -
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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