Contacts of the strand formed by residues 247 - 254 (chain A) in PDB entry 1MVW
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 GLY 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A PHE* 1.3 82.9 - - - +
248A MLY 1.3 67.2 + - - +
267A THR* 3.6 1.2 - - - -
268A TYR* 3.0 37.5 + - - -
269A LEU 4.4 0.4 + - - -
463A ASP* 3.3 11.2 - - - -
464A ILE* 4.2 16.8 - - - -
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Residues in contact with MLY 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A THR* 3.3 33.0 - - - -
189A THR* 4.8 13.7 - - + -
190A MLY 4.8 9.4 - - - -
193A ILE* 5.6 2.0 - - - -
226A ASN* 2.8 42.3 - - - -
229A LEU* 5.4 9.9 - - + +
230A GLU* 5.0 5.4 - - - -
234A ASN* 5.9 0.4 - - - -
244A SER* 4.6 7.0 - - - -
246A PHE* 4.0 26.5 - - + -
247A GLY* 1.3 78.6 - - - +
249A PHE* 1.3 64.5 - - - +
250A ILE* 3.8 32.3 - - + -
265A ILE* 4.5 14.6 - - + -
266A GLU 3.3 11.0 - - - +
268A TYR* 4.1 7.2 - - - -
461A VAL 3.7 0.8 - - - +
462A LEU* 3.5 3.3 - - - +
463A ASP* 2.4 63.9 + - + +
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Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A SER* 5.5 1.1 - - - -
248A MLY 1.3 77.6 - - - +
250A ILE* 1.3 61.1 + - - +
251A ARG* 4.0 26.2 - - + -
264A ASP 3.0 12.8 - - - +
266A GLU* 3.1 27.0 + - + +
268A TYR* 3.8 22.0 - - + +
458A PHE* 4.7 5.2 - + - -
460A GLY* 3.9 28.3 - - - -
461A VAL 3.5 6.3 - - - -
462A LEU* 3.6 28.7 - - + -
660A LEU* 3.9 18.8 - - + -
663A ASN* 4.2 21.5 - - + -
664A LEU* 4.0 24.9 - - + -
667A THR* 6.0 0.4 - - - -
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Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A THR* 5.0 3.6 - - + -
193A ILE* 3.1 34.5 - - + -
222A ILE* 6.0 1.3 - - + -
226A ASN* 5.4 0.7 - - - +
248A MLY 3.8 39.7 - - + -
249A PHE* 1.3 76.3 - - - +
251A ARG* 1.3 71.5 + - - +
252A ILE* 4.3 13.9 - - + +
263A ALA* 4.3 5.8 - - + -
264A ASP 3.2 18.6 - - - +
265A ILE* 4.3 15.9 - - + -
459A ILE 3.5 2.8 - - - +
460A GLY* 3.3 5.2 - - - -
461A VAL* 3.1 37.6 + - + +
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Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A PHE* 4.0 20.6 - - + -
250A ILE* 1.3 79.5 - - - +
252A ILE* 1.3 62.2 + - - +
253A HIS* 3.1 46.2 + - + -
263A ALA* 3.0 22.0 - - - -
264A ASP* 3.0 42.2 + - + -
458A PHE* 3.7 35.7 - - + -
459A ILE 4.0 2.5 - - - -
663A ASN* 3.6 34.6 + - - +
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ILE* 3.9 33.2 - - + -
196A PHE* 4.6 20.2 - - + -
222A ILE* 5.0 6.3 - - + -
250A ILE* 3.6 11.4 + - + -
251A ARG* 1.3 72.1 - - - +
253A HIS* 1.3 61.5 - - - +
254A PHE* 3.3 25.0 - - + -
260A LEU* 3.2 35.7 - - + -
262A SER 3.4 4.7 - - - +
263A ALA* 4.6 7.9 - - + -
458A PHE* 3.0 3.3 - - - -
459A ILE 2.7 43.6 + - - +
461A VAL* 4.6 10.8 - - + -
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Residues in contact with HIS 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG* 3.1 66.2 + - + -
252A ILE* 1.3 72.4 - - - +
254A PHE* 1.3 63.5 + - - +
260A LEU* 4.4 0.2 - - - -
261A ALA* 2.9 25.6 + - - +
262A SER* 2.4 38.1 + - - +
263A ALA 4.3 0.4 + - - -
264A ASP* 3.6 10.2 + - - -
455A ARG* 4.2 33.5 + - + -
457A TYR 3.5 6.1 - - - +
458A PHE* 3.6 20.7 - + + +
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Residues in contact with PHE 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 4.1 11.2 - + - -
166A MET* 3.0 40.6 - - + -
196A PHE* 3.6 32.5 - + + -
200A ALA* 4.3 7.9 - - + -
252A ILE* 3.3 29.2 - - + -
253A HIS* 1.3 77.4 - - - +
255A GLY* 1.3 67.2 + - - +
258A GLY* 3.9 21.1 - - - +
259A LYS 4.2 0.7 - - - -
260A LEU* 3.7 29.8 - - + -
261A ALA* 4.2 0.9 - - - -
455A ARG* 3.8 3.5 - - - -
456A GLN 3.4 12.8 + - - -
457A TYR 2.7 17.4 + - - +
459A ILE* 3.3 25.8 - - + -
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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