Contacts of the strand formed by residues 200 - 204 (chain A) 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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A VAL* 3.4 16.8 - - + -
141A ILE* 3.8 32.8 - - + -
195A TRP* 3.1 28.4 + - + +
196A ALA* 3.3 21.1 + - - +
199A GLY* 1.3 77.2 - - - +
201A LEU* 1.3 61.9 + - - +
202A LEU* 3.3 17.4 + - + +
299A ILE* 3.8 40.2 - - + -
301A TRP* 4.2 7.9 - - + -
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Residues in contact with LEU 201 (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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89A TRP* 3.9 27.1 - - + -
128A TRP* 3.9 33.2 - - + +
137A VAL* 4.1 13.7 - - + -
139A VAL 2.7 16.7 + - - +
140A VAL* 4.1 13.7 - - + -
141A ILE* 2.8 32.4 + - - +
199A GLY 3.4 2.6 + - - -
200A VAL* 1.3 69.6 - - - +
202A LEU* 1.3 63.6 + - - +
203A LEU* 3.9 24.0 - - + -
229A VAL* 4.4 0.9 - - + -
230A VAL* 6.5 0.2 - - + -
233A LEU* 3.5 31.4 - - + -
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Residues in contact with LEU 202 (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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128A TRP* 4.1 9.5 - - - +
141A ILE* 3.8 32.5 - - + -
155A GLY 4.2 1.2 - - - +
156A LEU* 3.6 29.3 - - + +
157A CYS* 3.0 48.8 + - - +
158A PHE* 5.7 0.9 - - + -
192A LEU* 3.8 39.3 - - + +
195A TRP* 4.3 11.4 - - + -
196A ALA* 4.4 5.8 - - + +
200A VAL* 3.3 21.1 + - + +
201A LEU* 1.3 76.8 - - - +
203A LEU* 1.3 55.7 + - - +
204A ASN 3.9 0.7 + - - -
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Residues in contact with LEU 203 (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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128A TRP* 3.6 47.8 - - + +
141A ILE 3.0 9.1 + - - -
142A LEU* 3.4 28.0 - - + +
143A GLY 2.8 23.8 + - - +
157A CYS* 4.3 0.7 - - - -
201A LEU* 3.5 18.4 + - + -
202A LEU* 1.3 72.2 - - - +
204A ASN* 1.3 77.4 + - - +
207A LEU* 4.3 0.2 - - + -
226A THR* 4.1 21.1 - - + +
229A VAL* 3.9 28.7 - - + -
230A VAL* 4.3 4.0 - - + -
252A LYS* 5.4 1.3 - - - +
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Residues in contact with ASN 204 (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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1A 3FL 2.7 43.7 + - - -
143A GLY* 3.3 10.0 - - - -
144A GLN 3.3 3.2 + - - +
145A ASP 4.1 5.6 - - - -
146A PRO* 3.6 19.8 - - + +
155A GLY* 5.8 1.8 - - - -
156A LEU 4.7 2.2 + - - +
157A CYS* 3.1 19.9 - - - +
202A LEU 3.9 2.8 + - - -
203A LEU* 1.3 77.7 - - - +
205A ALA* 1.3 64.4 + - - +
206A VAL 3.4 16.4 - - - +
207A LEU* 3.2 25.9 - - + +
226A THR* 3.4 9.7 - - - +
252A LYS* 5.5 0.2 - - - -
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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