Contacts of the strand formed by residues 192 - 198 (chain C) in PDB entry 3F12
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 192 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C VAL* 3.0 6.6 - - - +
152C ASP* 2.4 48.6 + - - +
153C ASN* 4.4 8.1 - - + +
191C LYS* 1.3 77.9 - - + +
193C TYR* 1.3 72.0 + - - +
194C ALA* 4.4 11.7 - - + -
209C SER* 4.4 7.4 - - - +
210C PHE 3.4 4.5 - - - +
211C ASN* 3.0 28.3 - - - +
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Residues in contact with TYR 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ILE* 5.0 0.5 - - - +
133C VAL* 4.5 11.9 - - + -
149C TRP* 5.2 4.0 - - + -
150C LYS 3.8 1.6 - - - -
151C VAL* 3.5 32.1 - - + +
180C LEU* 4.6 2.7 - - + -
182C LEU* 3.9 16.6 - - + -
186C ASP 3.9 3.3 + - - -
187C TYR* 2.4 64.1 + + - -
190C HIS* 4.1 9.1 + - + +
191C LYS 3.7 16.4 - - - -
192C VAL* 1.3 73.3 - - - +
194C ALA* 1.3 52.7 + - - +
209C SER* 2.5 30.2 - - - -
210C PHE* 3.0 47.7 + + + -
212C ARG* 3.7 17.9 - - + -
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Residues in contact with ALA 194 (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 TRP* 3.2 14.0 - - - -
150C LYS* 2.6 57.6 + - + +
192C VAL* 4.4 8.3 - - + -
193C TYR* 1.3 74.8 - - - +
195C CYS* 1.3 60.5 - - - +
196C GLU 4.0 0.7 - - - +
207C THR* 4.0 15.0 - - + -
209C SER* 3.4 15.3 - - - +
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Residues in contact with CYS 195 (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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116C VAL* 4.8 2.9 - - + +
118C ILE* 4.2 2.9 - - + -
135C CYS* 2.0 52.7 - - + -
147C VAL* 4.2 19.1 - - - -
148C GLN 3.7 2.9 - - - -
149C TRP* 4.1 16.6 - - + -
194C ALA* 1.3 73.9 - - - +
196C GLU* 1.3 59.6 + - - +
197C VAL* 3.7 8.5 + - - +
206C VAL 3.7 0.3 - - - +
207C THR* 3.6 7.1 - - - -
208C LYS 3.2 31.5 + - - +
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Residues in contact with GLU 196 (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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146C LYS* 3.3 4.9 - - - +
147C VAL* 3.5 1.1 - - - -
148C GLN* 2.6 61.9 + - + +
150C LYS* 3.3 36.6 + - + -
194C ALA* 4.0 0.4 - - + -
195C CYS* 1.3 70.3 - - - +
197C VAL* 1.3 61.5 - - - +
198C THR* 4.1 3.2 + - - +
205C PRO* 4.5 22.9 - - + +
206C VAL 3.5 9.0 - - - +
207C THR* 3.7 16.0 + - + +
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Residues in contact with VAL 197 (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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114C PRO* 3.7 29.2 - - + -
116C VAL* 3.9 19.5 - - + -
137C LEU* 3.4 42.4 - - + -
145C ALA* 4.6 0.9 - - + -
146C LYS 3.2 3.4 - - - +
147C VAL* 4.2 7.0 - - + -
195C CYS* 3.7 9.4 + - - +
196C GLU* 1.3 74.4 - - - +
198C THR* 1.3 70.0 + - - +
202C LEU* 3.8 11.4 - - + +
205C PRO* 3.4 6.1 - - - +
206C VAL 2.9 33.8 + - - +
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Residues in contact with THR 198 (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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145C ALA* 3.3 7.6 - - - +
146C LYS* 2.8 57.1 + - + -
196C GLU* 5.0 4.2 + - - +
197C VAL* 1.3 74.7 + - - +
199C HIS* 1.3 69.6 + - - +
202C LEU* 4.8 0.4 - - - -
205C PRO* 3.4 24.6 - - - +
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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