Contacts of the strand formed by residues 159 - 163 (chain C) in PDB entry 1F11
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 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C VAL* 5.7 2.2 - - + +
148C TRP* 3.7 20.0 - - + +
155C ARG 4.5 7.4 - - - +
156C GLN 3.0 28.9 - - - +
157C ASN 4.0 2.9 - - - +
158C GLY* 1.3 82.1 - - - +
160C LEU* 1.3 74.5 + - - +
161C ASN* 3.8 14.1 + - - +
177C SER* 3.4 24.2 - - - +
178C THR 3.4 4.5 - - - +
179C LEU* 4.5 6.1 - - + +
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Residues in contact with LEU 160 (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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158C GLY 4.7 4.7 - - - +
159C VAL* 1.3 85.5 - - - +
161C ASN* 1.3 62.9 - - - +
162C SER* 5.2 0.7 - - - -
176C SER* 3.4 5.2 + - - +
178C THR* 3.0 42.4 + - - +
180C THR* 4.9 9.2 - - - +
177D VAL* 4.0 28.0 - - + +
178D LEU 5.8 1.6 - - - +
179D GLN* 3.8 41.7 - - + +
186D THR* 5.0 5.8 - - + -
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Residues in contact with ASN 161 (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 VAL* 4.9 9.3 + - - +
159C VAL* 3.8 12.9 - - - +
160C LEU* 1.3 73.0 - - - +
162C SER* 1.3 63.0 + - - +
163C TRP* 3.7 34.2 - - + -
175C MET* 4.4 9.4 - - - -
176C SER 3.2 4.0 - - - +
177C SER* 2.8 33.1 + - - -
177D VAL* 3.8 11.0 - - - +
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Residues in contact with SER 162 (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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160C LEU 5.2 0.7 - - - -
161C ASN* 1.3 76.2 - - - +
163C TRP* 1.3 61.8 + - - +
175C MET* 3.3 3.6 - - - +
176C SER* 2.9 41.2 + - - -
174D PHE* 3.4 14.3 - - - -
175D PRO* 2.5 44.5 + - - +
177D VAL* 3.8 13.2 - - - +
187D LEU* 6.5 0.2 - - - -
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Residues in contact with TRP 163 (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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139C PHE* 4.2 9.0 - + - -
142C LYS* 3.8 46.5 + - + +
144C ILE* 4.6 12.2 - - - +
161C ASN* 3.7 34.5 - - + -
162C SER* 1.3 77.7 + - - +
164C THR* 1.3 66.3 + - - +
173C TYR* 5.3 0.7 - - + -
174C SER 3.5 3.8 - - - -
175C MET* 3.6 34.2 - - + +
174D PHE* 4.6 0.2 - - - -
175D PRO* 3.1 25.6 - - - +
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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