Contacts of the strand formed by residues 151 - 154 (chain C) in PDB entry 1F15
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 LEU 151 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PRO* 3.8 16.2 - - + +
57B THR* 4.0 1.3 - - - -
111C VAL* 4.8 10.8 - - + -
121C VAL 4.0 0.3 - - - +
122C TRP* 3.4 3.8 - - - -
123C VAL* 2.9 46.1 + - + +
150C VAL* 1.3 75.5 - - - +
152C VAL* 1.3 67.5 + - - +
153C TYR* 3.6 34.5 - - + +
161C GLN* 4.7 0.2 - - - +
163C ASN* 4.1 10.5 - - - +
164C ASN* 4.2 4.9 - - - +
165C LYS* 3.1 40.2 - - - +
166C LEU* 3.7 15.3 - - + -
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO 5.4 0.6 + - - -
57B THR* 3.3 30.2 + - + +
159B GLY* 5.7 0.4 - - - -
160B VAL* 4.6 15.5 - - + +
120C THR* 5.6 2.2 - - - +
121C VAL 3.5 3.6 - - - +
122C TRP* 3.8 36.8 - - + +
150C VAL* 4.0 13.0 - - + -
151C LEU* 1.3 83.1 - - - +
153C TYR* 1.3 60.9 + - - +
154C GLN* 3.4 19.9 + - + +
161C GLN* 3.2 15.8 + - - +
190C LYS* 5.6 1.6 - - - +
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Residues in contact with TYR 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PHE* 3.3 1.4 - - - -
111C VAL* 4.2 16.4 - - + -
113C PRO* 3.2 30.0 - - + +
117C PHE* 3.5 31.0 - + - -
120C THR* 3.2 3.9 - - - -
121C VAL* 2.9 50.8 + - + +
151C LEU* 3.6 13.1 - - + +
152C VAL* 1.3 69.3 - - - +
154C GLN* 1.3 60.5 + - - +
155C TYR* 5.8 0.4 - - - -
160C VAL* 3.0 21.9 - - + +
161C GLN* 2.8 51.3 + - + +
163C ASN 3.5 6.1 - - - -
164C ASN* 3.2 29.2 - - + -
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Residues in contact with GLN 154 (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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155B TYR* 4.8 2.6 + - - -
157B ALA 2.8 28.9 + - - -
158B SER* 3.0 19.5 + - - +
159B GLY* 3.0 22.6 - - - +
117C PHE* 4.5 2.9 - - - -
120C THR* 3.5 27.1 - - + +
152C VAL* 3.4 15.8 + - + +
153C TYR* 1.3 73.9 - - - +
155C TYR* 1.3 71.5 + - - +
156C ALA* 3.4 5.4 + - - +
161C GLN* 3.1 30.0 + - - +
190C LYS* 4.7 10.3 + - - +
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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