Contacts of the strand formed by residues 175 - 180 (chain u) in PDB entry 5OOM
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 MET 175 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92u PHE* 3.6 40.8 - - + +
93u ASP 3.4 24.0 - - - +
94u ILE* 4.1 25.4 - - - -
97u MET* 4.1 17.9 - - + -
121u THR* 3.3 3.4 - - - -
123u TYR* 3.0 27.8 - - + +
125u VAL* 4.9 7.0 - - + -
172u PHE* 2.7 49.8 + - + +
173u GLY 3.6 0.6 - - - -
174u SER* 1.3 83.3 - - - +
176u VAL* 1.3 56.4 + - - +
177u ILE* 5.4 1.1 - - + -
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Residues in contact with VAL 176 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L SER* 5.2 3.1 - - - -
120u TYR* 3.7 34.1 - - + +
121u THR* 3.7 11.9 - - + -
123u TYR 2.9 3.2 + - - +
124u PHE* 3.7 17.7 - - + -
125u VAL* 2.9 25.3 + - - +
170u VAL 3.3 20.0 - - - +
171u ASP* 3.8 19.3 - - + -
172u PHE* 5.7 0.2 - - - -
175u MET* 1.3 75.5 - - - +
177u ILE* 1.3 66.2 + - - +
178u HIS* 3.9 18.2 - - + +
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Residues in contact with ILE 177 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97u MET* 3.8 31.6 - - + -
101u LEU* 5.4 2.9 - - + -
125u VAL* 3.6 31.6 - - + -
127u VAL* 4.8 3.8 - - + -
142u VAL* 4.7 14.6 - - + -
169u CYS* 3.4 3.8 - - - +
170u VAL* 2.8 65.2 + - + +
172u PHE* 5.0 5.2 - - + -
175u MET* 5.4 1.3 - - + -
176u VAL* 1.3 78.4 - - - +
178u HIS* 1.3 61.3 + - - +
179u LEU* 3.7 34.8 - - + +
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Residues in contact with HIS 178 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L SER 3.9 15.9 - - - -
139L ALA* 4.1 5.1 - - + +
120u TYR* 5.3 1.4 + - - -
124u PHE* 3.3 41.4 - + - -
125u VAL 2.9 11.1 + - - -
126u ILE* 3.6 20.8 - - + -
127u VAL* 2.9 31.5 + - - +
167u TRP* 3.3 26.5 - + + -
168u LEU 3.5 4.7 - - - +
169u CYS* 3.3 26.2 - - + +
176u VAL* 3.9 16.2 - - + +
177u ILE* 1.3 74.8 - - - +
179u LEU* 1.3 61.4 + - - +
180u MET* 3.6 8.2 + - - +
190u LEU* 4.6 2.2 - - + -
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Residues in contact with LEU 179 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101u LEU* 5.0 3.1 - - + -
127u VAL* 3.1 26.7 - - + +
135u LEU* 3.4 36.2 - - + +
138u MET* 3.7 37.2 - - + +
139u ALA* 3.7 22.0 - - + -
142u VAL* 5.3 1.3 - - + -
166u ASP 3.9 0.5 - - - +
167u TRP 3.7 0.2 - - - -
168u LEU* 2.8 53.3 + - + +
177u ILE* 3.7 18.8 - - + +
178u HIS* 1.3 71.8 - - - +
180u MET* 1.3 59.1 + - - +
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Residues in contact with MET 180 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126u ILE* 3.7 29.6 - - + -
127u VAL 3.0 10.8 + - - +
128u SER* 3.2 20.0 - - - -
129u GLY 3.5 1.4 + - - -
135u LEU* 3.4 15.4 - - - +
166u ASP 3.3 16.6 - - - +
167u TRP* 3.6 34.1 - - + -
178u HIS* 4.4 8.1 - - - +
179u LEU* 1.3 78.1 - - - +
181u LEU* 1.3 66.4 + - - +
184u THR* 4.2 8.5 - - + +
185u ARG* 3.7 39.5 - - + +
188u TYR* 5.6 0.4 - - + -
190u LEU* 4.0 24.2 - - + -
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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