Contacts of the strand formed by residues 154 - 157 (chain C) in PDB entry 2P80
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 ILE 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LEU* 3.9 2.7 - - - -
73C MET* 3.2 30.3 - - + +
75C VAL* 5.5 1.8 - - + -
81C LEU* 4.3 8.7 - - + -
99C PHE* 3.5 34.5 - - + -
101C ALA* 3.7 31.0 - - + -
124C PHE* 4.0 20.0 - - + -
130C GLY 3.9 0.9 - - - +
131C VAL* 3.3 1.7 - - - +
132C PHE* 2.9 32.1 + - + +
134C TYR* 3.8 3.8 - - + -
153C ALA* 1.3 79.9 - - - +
155C MET* 1.3 60.9 + - - +
156C VAL* 3.9 17.5 - - + -
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Residues in contact with MET 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C HIS* 4.7 0.7 - - - +
72C LEU* 4.0 7.5 - - + +
73C MET 2.8 9.9 + - - -
74C VAL* 3.4 24.6 - - + +
75C VAL 3.1 22.3 + - - +
131C VAL* 3.4 30.1 - - + +
154C ILE* 1.3 73.5 - - - +
156C VAL* 1.3 63.7 + - - +
157C LEU* 3.5 44.2 - - + -
172C TYR* 4.5 2.5 - - - +
175C ILE* 3.3 28.9 - - + -
242C LEU* 3.9 10.5 - - - -
244C VAL* 3.9 12.8 - - - -
270C PHE* 4.3 8.1 - - + -
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C VAL* 3.0 9.4 - - + -
76C HIS 3.3 31.4 - - - +
77C GLN* 3.3 13.0 - - + +
101C ALA* 4.6 7.0 - - + -
126C ALA* 3.6 22.4 - - + -
128C LYS 3.6 21.1 - - - +
129C PRO* 3.3 4.7 - - - +
130C GLY 2.9 33.2 + - - +
154C ILE* 3.9 24.7 - - + -
155C MET* 1.3 71.6 - - - +
157C LEU* 1.3 60.3 + - - +
270C PHE* 3.3 3.5 - - - -
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Residues in contact with LEU 157 (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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28C HIS* 4.2 4.9 - - + -
29C SER 5.1 5.8 - - - +
30C GLN* 4.5 7.9 - - + +
74C VAL* 3.4 32.1 - - + -
75C VAL 2.9 8.8 + - - +
76C HIS* 3.2 30.8 - - + +
77C GLN 3.2 2.8 + - - -
129C PRO* 4.7 0.7 - - - -
155C MET* 3.5 28.7 - - + -
156C VAL* 1.3 74.3 - - - +
158C PRO* 1.3 74.9 - - + +
161C GLY* 5.3 1.1 - - - -
162C LEU* 3.3 42.0 - - + -
172C TYR* 4.1 13.9 - - + +
270C PHE* 3.5 9.9 - - + -
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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