Contacts of the strand formed by residues 142 - 151 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C LEU* 3.8 39.3 - - - -
104C LEU* 3.3 17.9 - - - +
105C GLY 4.5 3.6 - - - -
106C ILE* 3.8 33.9 - - + -
137C TYR* 2.9 19.1 + - + +
138C LYS* 3.4 16.0 + - - +
141C GLY* 1.3 79.0 - - - +
143C ASP* 1.3 61.7 + - - +
144C PHE 4.5 1.3 - - - +
182C ILE* 3.2 16.4 - - + +
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Residues in contact with ASP 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 3.8 30.0 - - + +
98C LYS* 4.4 10.0 + - - -
103C ILE* 3.9 23.3 - - + +
104C LEU 2.8 7.9 + - - +
138C LYS* 2.6 31.0 + - - +
141C GLY 4.0 8.3 + - - +
142C CYS* 1.3 77.7 - - - +
144C PHE* 1.3 60.4 + - - +
182C ILE* 3.7 10.3 - - - -
183C VAL 3.0 20.0 + - - -
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Residues in contact with PHE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.7 29.8 - - + -
29C ILE* 4.2 12.3 - - + -
75C GLY* 4.3 6.1 - - - -
76C VAL 4.0 11.4 - - - -
77C ILE* 3.5 30.7 - - + -
103C ILE* 3.7 20.9 - - + -
104C LEU 3.6 6.5 - - - +
105C GLY* 3.1 44.2 - - - -
106C ILE* 3.1 11.3 + - - +
142C CYS* 4.5 0.2 - - - +
143C ASP* 1.3 81.1 + - - +
145C ALA* 1.3 66.9 + - - +
182C ILE* 3.7 4.8 - - - +
183C VAL* 3.1 17.9 - - + +
185C ILE* 3.5 30.3 - - + -
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ILE* 3.2 12.8 - - + +
108C VAL* 4.3 11.4 - - + -
144C PHE* 1.3 80.2 - - - +
146C LYS* 1.3 60.8 + - - +
173C TYR* 3.3 7.9 - - + +
177C CYS* 3.7 20.6 - - - -
182C ILE* 3.5 19.1 - - + -
183C VAL 2.8 6.2 + - - +
185C ILE* 3.0 32.4 + - - +
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Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ALA* 5.6 0.2 - - - +
33C ASP* 2.7 28.1 + - - +
77C ILE* 4.0 33.8 - - + +
106C ILE 3.0 5.1 + - - -
107C LYS* 3.4 30.9 - - + +
108C VAL* 2.9 29.1 + - - +
109C ASP* 3.8 2.9 + - - +
145C ALA* 1.3 75.3 - - - +
147C TRP* 1.3 64.9 + - - +
148C ARG* 3.9 22.3 - - - +
173C TYR* 3.6 1.8 - - - -
185C ILE* 4.4 8.1 - - + +
187C GLU* 3.5 26.0 + - + +
229C LYS* 4.7 11.2 - - + +
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Residues in contact with TRP 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C VAL* 4.1 4.0 - - + -
109C ASP* 3.5 26.0 - - + -
124C THR* 3.4 41.1 - - + +
125C GLN 3.6 1.3 - - - -
126C GLY* 3.6 45.8 - - - -
127C LEU* 3.6 21.5 - - + -
130C LEU* 4.3 5.6 - - + -
146C LYS* 1.3 75.5 - - - +
148C ARG* 1.3 62.9 + - - +
149C CYS* 3.7 12.4 - - - -
169C VAL* 4.0 16.3 + - + +
170C LEU* 3.7 18.9 - - + +
173C TYR* 3.3 44.6 + + + -
185C ILE 4.0 2.9 + - - +
187C GLU* 3.2 29.2 + - - +
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Residues in contact with ARG 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ASP* 3.1 14.1 + - - +
112C VAL* 4.7 6.2 - - - +
124C THR* 2.8 29.2 + - - +
146C LYS* 3.9 15.2 - - - +
147C TRP* 1.3 76.3 - - - +
149C CYS* 1.3 63.3 + - - +
150C VAL* 3.3 21.0 + - + +
187C GLU* 3.4 27.1 + - + +
189C GLU* 3.0 27.8 + - - +
361C HIS* 3.0 52.1 + - - +
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Residues in contact with CYS 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C THR* 3.6 8.1 - - - -
147C TRP* 3.7 19.0 + - - -
148C ARG* 1.3 74.8 - - - +
150C VAL* 1.3 63.7 + - - +
151C LEU* 5.4 1.3 - - + -
166C ASN* 3.3 28.3 - - + +
169C VAL* 3.7 12.3 - - - -
170C LEU* 3.6 34.3 - - + -
187C GLU 2.9 12.9 + - - +
188C PRO* 4.5 3.6 - - + -
189C GLU* 2.9 30.7 + - - +
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Residues in contact with VAL 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C VAL* 4.5 13.3 - - + +
122C VAL* 3.8 25.7 + - + +
124C THR* 4.6 2.0 + - - -
148C ARG* 3.3 46.0 - - + +
149C CYS* 1.3 78.0 - - - +
151C LEU* 1.3 69.3 + - - +
152C LYS* 4.5 1.0 + - - +
162C SER* 4.9 0.5 + - - -
166C ASN* 4.3 2.4 + - - -
189C GLU* 3.4 3.4 - - + +
191C LEU* 3.6 29.2 - - + -
361C HIS* 4.4 0.9 - - + -
362C ALA* 3.3 36.0 - - + +
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C CYS* 5.4 2.2 - - + -
150C VAL* 1.3 75.9 - - - +
152C LYS* 1.3 62.1 + - - +
153C ILE 4.2 0.2 + - - -
158C PRO* 4.3 17.3 - - + -
162C SER* 3.3 36.1 - - - +
163C ILE* 4.6 3.8 - - + +
166C ASN* 3.8 25.1 - - + +
188C PRO* 4.8 9.6 - - + -
189C GLU 2.8 11.3 + - - +
190C VAL* 3.5 13.2 - - + +
191C LEU* 2.9 30.0 + - - +
208C VAL* 3.2 45.1 - - + -
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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