Contacts of the strand formed by residues 148 - 152 (chain A) in PDB entry 3CFV
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 VAL 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ALA* 5.5 0.9 - - + -
141A THR 3.6 12.6 - - - +
142A LYS* 3.7 30.7 - - + +
146A SER 4.4 3.1 - - - +
147A ASP* 1.3 75.7 - - - +
149A LEU* 1.3 63.5 + - - +
171A ARG* 3.9 1.0 - - - -
172A LEU* 2.9 60.9 + - + +
175A HIS* 4.3 5.8 - - - +
182A LEU* 5.3 1.8 - - + -
192A LEU* 4.2 9.6 - - + -
194A SER* 3.8 12.3 - - - +
204A TRP* 3.9 18.6 - - + -
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Residues in contact with LEU 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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122A HIS* 4.1 5.6 - - + -
123A GLU* 5.3 3.8 - - + +
140A ALA* 3.2 4.9 - - - +
141A THR* 2.8 44.0 + - + +
143A THR* 3.6 27.6 - - + -
147A ASP* 4.4 9.4 - - + +
148A VAL* 1.3 80.8 - - - +
150A VAL* 1.3 64.2 + - - +
151A PHE* 3.7 19.7 - - + -
166A CYS* 4.1 9.4 - - - -
168A PRO* 3.7 33.7 - - + -
170A LEU 3.5 4.5 - - - +
171A ARG* 4.0 26.5 - - + +
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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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138A ILE* 3.8 26.7 - - + -
139A ILE 3.5 4.7 - - - +
140A ALA* 4.5 10.3 - - + -
149A LEU* 1.3 79.8 - - - +
151A PHE* 1.3 67.2 + - - +
152A ASP* 6.3 0.4 - - + -
168A PRO* 3.9 0.7 - - - +
169A ASP* 3.0 29.4 + - + +
170A LEU* 3.0 37.6 + - + -
172A LEU* 4.0 25.1 - - + -
184A TRP* 4.6 4.9 - - + -
206A ILE* 4.6 14.6 - - + -
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Residues in contact with PHE 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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78A LEU* 3.9 24.0 - - + -
120A ILE* 3.9 28.3 - - + -
121A ASN 4.2 6.1 - - - -
122A HIS* 3.8 14.6 - - + -
137A HIS 3.6 1.2 - - - +
138A ILE* 3.3 3.6 - - - +
139A ILE* 2.7 44.7 + - + +
141A THR* 3.4 33.7 - - + -
149A LEU* 3.7 13.9 - - + -
150A VAL* 1.3 78.1 - - - +
152A ASP* 1.3 58.8 + - - +
153A TYR 3.8 1.1 + - - +
156A HIS* 3.7 23.6 - + - +
166A CYS* 3.9 22.0 - - - -
167A ASN 4.2 2.2 - - - -
168A PRO* 3.8 22.4 - - + -
169A ASP* 3.5 1.6 - - - -
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Residues in contact with ASP 152 (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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137A HIS* 3.1 27.9 + - - +
138A ILE* 4.5 11.8 - - + +
150A VAL* 6.3 0.2 - - + -
151A PHE* 1.3 71.6 - - - +
153A TYR* 1.3 57.7 + - - +
154A THR* 2.6 31.8 + - - -
155A LYS* 2.8 49.1 + - + +
156A HIS* 3.0 12.5 - - - -
169A ASP* 3.0 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