Contacts of the strand formed by residues 187 - 193 (chain C) in PDB entry 1M7X
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 187 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C GLY* 3.6 16.5 - - - -
155C GLN* 4.2 32.7 + - + +
156C PHE* 4.1 8.1 - - - -
159C TRP* 4.6 8.5 - - + -
185C GLY 3.9 11.9 - - - +
186C GLN* 1.3 72.3 - - - +
188C TYR* 1.3 65.5 + - - +
211C GLN* 3.0 43.3 - - + +
217C ALA* 4.1 7.9 - - + -
218C SER 3.4 10.8 - - - +
219C LEU* 4.2 17.5 - - + -
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Residues in contact with TYR 188 (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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127C ALA* 3.4 18.2 + - + +
140C PHE* 3.6 23.3 - + + -
152C VAL* 4.7 5.6 - - + -
153C VAL 3.4 14.1 - - - +
156C PHE* 4.8 5.2 - - + -
159C TRP* 4.2 3.6 - - - -
186C GLN 4.0 0.4 - - - -
187C LEU* 1.3 78.2 - - - +
189C LYS* 1.3 74.6 + - - +
190C TYR* 3.5 31.6 - + - -
204C ASP* 2.6 24.3 + - + +
206C TYR 5.3 0.2 + - - -
207C ALA* 4.7 3.8 - - - -
217C ALA* 3.7 1.2 - - - +
218C SER* 2.9 67.4 + - - +
219C LEU 3.8 14.3 + - - -
220C ILE* 3.7 23.8 - - + -
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Residues in contact with LYS 189 (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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151C SER 3.7 1.0 - - - +
152C VAL* 3.8 3.8 - - - -
153C VAL* 3.0 33.2 + - + -
159C TRP* 4.0 25.1 - - + -
188C TYR* 1.3 88.5 - - - +
190C TYR* 1.3 69.0 + - - +
191C GLU 4.1 0.4 - - - -
201C LEU* 4.7 29.5 + - + +
202C LYS 3.4 18.2 - - - +
203C SER* 4.5 11.0 - - - +
216C THR* 3.4 30.3 + - - +
217C ALA* 3.8 12.1 - - + -
218C SER* 4.1 4.5 - - - +
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Residues in contact with TYR 190 (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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126C GLY 4.0 3.8 - - - -
140C PHE* 3.5 22.8 - + - +
141C SER 3.3 19.3 + - - -
142C VAL* 4.2 21.3 - - + -
150C VAL* 4.1 11.7 - - + -
151C SER 3.2 8.7 - - - +
152C VAL* 4.0 13.0 - - + -
166C MET* 3.8 32.1 - - + -
188C TYR* 3.5 14.5 - + - -
189C LYS* 1.3 82.8 - - - +
191C GLU* 1.3 62.1 - - - +
192C MET* 3.5 2.1 + - + +
200C ARG 3.4 1.4 - - - +
201C LEU* 4.7 1.8 - - - -
202C LYS* 3.1 37.8 + - + +
203C SER 4.8 2.5 - - - -
204C ASP* 3.4 48.3 + - + -
351C PHE* 6.0 1.6 - + + -
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Residues in contact with GLU 191 (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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149C ARG* 2.6 32.4 + - - +
150C VAL* 3.2 2.3 - - - -
151C SER* 2.6 39.7 + - - +
153C VAL* 4.0 17.4 - - + +
159C TRP 4.8 5.2 - - - +
160C ASP* 4.8 0.2 - - - -
161C GLY* 3.3 31.1 + - - -
189C LYS 4.1 1.4 - - - -
190C TYR* 1.3 70.5 - - - +
192C MET* 1.3 59.2 + - - +
199C LEU* 4.2 19.5 - - + +
200C ARG 3.5 5.4 - - - +
201C LEU* 4.0 22.8 - - + +
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Residues in contact with MET 192 (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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144C ALA* 4.9 3.1 - - + -
147C ALA* 3.9 11.7 - - - -
149C ARG 3.0 11.4 - - - +
150C VAL* 3.7 17.3 - - + -
190C TYR* 4.5 2.0 - - + +
191C GLU* 1.3 75.8 - - - +
193C ILE* 1.3 74.1 + - - +
194C ASP* 4.4 7.4 - - - +
199C LEU* 3.5 2.3 - - - +
200C ARG* 2.8 48.6 + - + +
202C LYS* 3.4 33.0 - - + +
350C GLU 5.4 0.2 - - - +
351C PHE* 4.1 17.3 - - + -
352C ASP* 3.2 44.2 - - - +
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Residues in contact with ILE 193 (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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147C ALA* 3.3 6.4 - - - +
148C ARG* 2.9 29.4 + - + +
149C ARG* 2.9 65.9 + - + +
192C MET* 1.3 88.7 - - - +
194C ASP* 1.3 70.0 + - - +
197C GLY* 3.4 24.7 - - - +
198C ASN 2.8 17.9 - - - +
199C LEU* 4.2 11.0 - - + -
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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