Contacts of the strand formed by residues 181 - 186 (chain A) in PDB entry 2FIN
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 GLY 181 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLU* 3.7 12.3 - - - -
144A VAL 2.8 22.1 + - - -
179A ILE 3.0 2.4 + - - -
180A ILE* 1.3 75.6 - - - +
182A SER* 1.3 56.3 + - - -
183A THR* 3.7 2.1 - - - +
14B SER* 2.4 32.1 + - - -
15B TYR 3.9 13.9 - - - -
16B THR* 4.3 7.0 - - - -
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Residues in contact with SER 182 (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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144A VAL 4.2 1.8 + - - -
145A SER* 4.0 3.0 - - - +
146A ILE 3.2 25.8 + - - +
181A GLY* 1.3 72.7 + - - -
183A THR* 1.3 66.6 + - - +
184A ILE* 4.2 5.5 + - - +
14B SER 3.3 13.9 + - - -
15B TYR 4.3 2.8 - - - -
16B THR* 4.3 2.2 - - - +
49B GLN 4.8 1.7 + - - -
50B VAL* 3.9 21.9 - - - +
51B CYS* 3.0 47.3 + - - -
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.7 17.9 - - + -
180A ILE* 3.4 31.0 - - + -
182A SER* 1.3 84.2 + - - +
184A ILE* 1.3 61.0 + - - +
185A VAL* 4.0 5.8 + - - +
195A PHE* 4.6 24.0 - - + -
215A PHE* 6.2 0.9 - - + -
13B PHE* 3.0 38.7 - - - +
14B SER* 3.5 16.5 + - - +
51B CYS* 5.0 2.2 - - - -
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Residues in contact with ILE 184 (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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146A ILE 3.4 4.1 + - - +
147A ASP* 3.0 55.4 + - + +
148A ILE 3.4 3.6 + - - +
182A SER* 4.1 7.3 + - - +
183A THR* 1.3 71.7 - - - +
185A VAL* 1.3 73.9 + - - +
186A ASP* 5.4 4.0 - - - +
10B ALA* 3.2 46.4 - - + +
11B CYS 4.1 10.5 - - - +
12B CYS* 4.9 5.8 - - - +
13B PHE* 4.8 0.4 - - + -
31B THR* 6.1 0.2 - - + -
49B GLN* 4.9 14.6 - - + +
51B CYS* 5.1 4.7 - - - -
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 5.9 2.9 - - + -
148A ILE* 3.4 24.9 - - + -
183A THR* 4.0 13.9 + - - +
184A ILE* 1.3 91.4 - - - +
186A ASP* 1.3 60.3 + - - +
187A THR 3.0 7.7 + - - +
190A VAL* 4.0 16.2 - - + -
193A LEU* 4.1 15.5 - - + -
195A PHE* 5.2 5.2 - - + -
217A TYR* 4.2 32.3 - - + +
9B THR 3.8 12.6 - - - +
10B ALA* 4.5 4.2 - - - -
13B PHE* 4.9 9.7 - - + -
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Residues in contact with ASP 186 (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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147A ASP* 4.8 2.1 - - - +
148A ILE 3.3 19.7 + - - +
149A ARG* 3.6 24.7 + - - +
150A CYS* 5.4 2.9 - - + +
184A ILE* 5.6 4.4 - - - +
185A VAL* 1.3 68.2 - - - +
187A THR* 1.3 55.4 + - - +
188A LYS* 2.7 33.5 + - + +
189A CYS* 2.8 14.9 + - + +
190A VAL* 3.3 10.5 - - - +
9B THR 5.0 2.2 - - - -
10B ALA* 4.6 12.9 - - - +
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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