Contacts of the strand formed by residues 139 - 143 (chain B) in PDB entry 3FCL
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 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B VAL* 3.6 2.0 - - - +
138B LYS* 1.3 85.7 - - + +
140B VAL* 1.3 67.7 + - - +
141B ILE* 4.1 3.1 - - + -
199B GLY 3.2 2.9 + - - +
200B VAL* 4.1 23.1 - - + -
201B LEU 2.8 30.1 + - - -
241B VAL* 3.3 13.2 - - + +
243B LEU* 4.4 14.8 - - + -
287B THR* 3.6 32.5 - - + -
291B LEU* 3.9 8.3 - - + -
299B ILE* 3.9 21.1 - - + -
301B TRP* 4.6 4.0 - - + -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 3.9 17.5 - - + -
139B VAL* 1.3 78.6 - - - +
141B ILE* 1.3 59.1 + - - +
142B LEU* 3.5 30.1 + - + +
201B LEU* 3.6 22.2 - - + +
230B VAL* 5.4 1.6 - - + -
233B LEU* 4.0 14.4 - - + -
240B LEU* 4.5 4.7 - - + -
241B VAL 2.8 9.6 + - - +
242B PHE* 3.4 37.6 - - + -
243B LEU 2.7 33.8 + - - +
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Residues in contact with ILE 141 (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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139B VAL* 4.1 1.8 - - + -
140B VAL* 1.3 72.8 - - - +
142B LEU* 1.3 61.4 + - - +
157B CYS* 3.5 15.0 - - - -
158B PHE* 4.3 3.6 - - + -
195B TRP* 4.5 7.0 - - + -
200B VAL* 3.9 23.8 - - + -
201B LEU 2.8 11.4 + - - +
202B LEU* 4.0 13.9 - - + -
203B LEU* 3.0 27.9 + - - +
243B LEU* 3.5 26.7 - - + +
245B TRP* 3.7 48.9 - - + -
301B TRP* 4.4 14.8 - - + -
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Residues in contact with LEU 142 (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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140B VAL* 3.5 27.8 - - + +
141B ILE* 1.3 76.4 - - - +
143B GLY* 1.3 60.4 + - - +
158B PHE* 4.8 0.2 - - - -
203B LEU* 3.2 31.6 - - + +
204B ASN 5.7 1.6 - - - -
230B VAL* 4.4 13.0 - - + -
242B PHE* 5.0 2.7 - - + -
243B LEU 3.0 7.5 + - - +
244B LEU* 3.3 30.3 - - + -
245B TRP* 3.3 18.7 + - - +
249B ALA* 3.2 35.7 - - + +
252B LYS* 3.9 25.1 - - + -
253B GLY* 4.6 3.8 - - - +
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Residues in contact with GLY 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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2B 3FL 3.4 8.7 - - - -
141B ILE 4.1 0.2 + - - -
142B LEU* 1.3 76.5 - - - +
144B GLN* 1.3 60.1 + - - -
157B CYS* 4.6 1.6 - - - -
158B PHE* 4.4 8.1 - - - -
203B LEU 2.8 11.5 + - - -
204B ASN* 3.3 14.1 - - - -
205B ALA* 3.0 24.0 + - - +
245B TRP 4.3 4.5 - - - -
249B ALA* 4.0 13.4 - - - +
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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