Contacts of the strand formed by residues 133 - 140 (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 133 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ILE* 3.6 10.1 - - + -
119C PHE 3.4 15.9 - - - +
121C PRO* 3.8 20.0 - - + -
132C SER* 1.3 74.6 - - - +
134C VAL* 1.3 57.5 + - - +
149C TRP* 3.4 32.3 - - + -
178C SER 3.4 4.0 - - - +
179C THR* 3.6 0.9 - - - -
180C LEU* 3.2 47.1 + - + +
182C LEU* 4.5 6.7 - - + -
187C TYR* 4.4 10.8 - - + -
193C TYR* 4.5 7.2 - - + -
210C PHE* 3.7 14.6 - - + -
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Residues in contact with VAL 134 (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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118C ILE* 3.7 5.2 - - - +
119C PHE* 3.1 58.4 + - + +
132C SER 3.7 4.4 + - - +
133C VAL* 1.3 75.4 - - - +
135C CYS* 1.3 72.6 + - - +
136C LEU* 5.0 0.7 - - + -
149C TRP* 4.0 0.7 - - - -
177C SER* 4.0 19.3 - - - +
178C SER 3.4 8.3 - - - +
179C THR* 4.2 8.5 - - + +
136D LEU* 4.2 17.3 - - + -
153D LEU* 3.2 34.8 - - + -
191D SER* 4.8 4.0 - - - +
193D VAL* 5.8 0.9 - - + -
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Residues in contact with CYS 135 (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* 4.3 8.1 - - - -
117C PHE 3.5 16.2 - - - -
118C ILE* 4.6 0.7 - - + -
134C VAL* 1.3 79.0 - - - +
136C LEU* 1.3 58.8 + - - +
137C LEU* 3.8 16.2 - - + +
149C TRP* 3.3 19.7 - - + -
176C LEU 3.3 6.2 - - - +
177C SER* 3.8 0.2 - - - -
178C SER* 3.0 28.6 + - - +
195C CYS* 2.0 50.0 - - - -
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Residues in contact with LEU 136 (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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115C SER 3.5 2.6 - - - +
116C VAL* 3.6 2.6 - - - +
117C PHE* 3.0 45.2 + - + +
119C PHE* 3.6 32.4 - - + -
134C VAL* 4.1 3.2 - - + -
135C CYS* 1.3 72.9 - - - +
137C LEU* 1.3 75.6 + - - +
138C ASN* 4.1 24.9 - - + +
175C SER* 4.7 1.6 - - - -
176C LEU 3.4 2.7 - - - +
177C SER* 4.5 1.8 - - - +
149D ALA* 4.2 9.2 - - + -
178D PHE* 3.4 37.0 - - + -
193D VAL* 3.9 23.8 - - + -
195D THR* 5.4 0.7 - - + -
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Residues in contact with LEU 137 (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* 3.8 8.5 - - + -
115C SER 3.8 4.3 - - - -
116C VAL* 4.6 1.3 - - + +
135C CYS* 3.8 17.9 - - - +
136C LEU* 1.3 78.9 - - - +
138C ASN* 1.3 58.5 - - - +
140C PHE* 3.0 25.4 - - + -
145C ALA* 3.8 22.4 - - + -
146C LYS 5.0 0.4 - - - +
147C VAL* 3.9 20.2 - - + -
175C SER* 3.2 1.4 - - - -
176C LEU* 2.7 48.2 + - + +
197C VAL* 3.4 48.2 - - + -
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Residues in contact with ASN 138 (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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113C ALA 4.2 0.2 - - - +
115C SER* 3.0 49.0 + - - +
117C PHE* 4.5 4.4 - - + -
136C LEU* 3.8 21.5 - - + +
137C LEU* 1.3 71.2 - - - +
139C ASN* 1.3 91.4 + - - +
140C PHE* 4.1 1.1 - - - -
175C SER* 2.4 34.4 + - - -
176D HIS* 3.2 12.6 + - - -
193D VAL* 5.8 0.4 - - - -
195D THR* 2.9 34.5 - - - +
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Residues in contact with ASN 139 (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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112C ALA* 3.6 11.9 - - + +
113C ALA 3.5 10.6 - - - +
115C SER* 5.6 1.1 - - - +
138C ASN* 1.3 115.0 + - - +
140C PHE* 1.3 59.0 + - - +
171C ASP* 2.7 30.4 + - - -
173C THR* 3.5 16.6 - - + +
174C TYR 3.2 12.6 + - - -
175C SER* 3.4 0.6 + - - -
176D HIS* 3.9 10.3 - - - -
195D THR* 5.4 0.2 - - - +
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Residues in contact with PHE 140 (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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112C ALA* 3.6 15.3 - - - +
114C PRO* 3.5 30.1 - - + -
137C LEU* 3.0 38.8 - - + -
139C ASN* 1.3 76.1 - - - +
141C TYR* 1.3 60.0 + - - +
142C PRO 3.5 11.9 - - - -
143C ARG 3.7 23.1 - - - -
145C ALA* 4.2 14.4 - - + -
164C VAL* 5.2 0.9 - - + -
173C THR* 3.4 7.2 - - - -
174C TYR* 2.9 61.2 + - + -
175C SER* 3.6 4.9 - - - -
176C LEU* 3.8 24.5 - - + -
199C HIS* 3.6 14.8 - + - +
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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