Contacts of the strand formed by residues 247 - 254 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246P PHE* 1.3 83.7 - - - +
248P MLY 1.3 67.8 + - - +
267P THR* 3.6 1.2 - - - -
268P TYR* 3.0 36.7 + - - -
269P LEU* 4.4 0.6 + - - +
463P ASP* 3.3 11.0 - - - -
464P ILE* 4.2 16.2 - - - -
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Residues in contact with MLY 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P THR* 3.3 33.2 - - - -
189P THR* 4.8 13.2 - - - -
190P MLY 4.8 9.4 - - - -
193P ILE* 5.6 1.6 - - - -
226P ASN* 2.8 42.7 - - - -
229P LEU* 5.4 9.4 - - + +
230P GLU* 5.0 6.3 - - - -
234P ASN* 5.9 0.4 - - - -
244P SER* 4.6 6.5 - - - -
246P PHE* 4.0 25.4 - - + -
247P GLY* 1.3 77.7 - - - +
249P PHE* 1.3 64.3 + - - +
250P ILE* 3.8 32.8 - - + -
265P ILE* 4.5 15.0 - - + -
266P GLU 3.3 11.2 - - - +
267P THR* 4.9 0.4 - - - -
268P TYR* 4.1 6.8 - - - -
461P VAL 3.7 1.2 - - - +
462P LEU* 3.5 3.7 - - - +
463P ASP* 2.4 64.1 + - + +
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Residues in contact with PHE 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174P SER* 5.5 1.6 - - - -
248P MLY 1.3 78.0 - - - +
250P ILE* 1.3 61.2 + - - +
251P ARG* 4.0 26.9 - - + -
264P ASP 3.0 12.6 - - - +
266P GLU* 3.1 24.4 + - + +
268P TYR* 3.8 23.8 - - + +
458P PHE* 4.7 4.9 - + - -
460P GLY* 3.9 29.8 - - - -
461P VAL 3.5 6.3 - - - -
462P LEU* 3.6 28.0 - - + -
660P LEU* 3.9 18.6 - - + -
663P ASN* 4.2 21.1 - - + -
664P LEU* 4.0 24.9 - - + -
667P THR* 6.0 0.2 - - - -
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Residues in contact with ILE 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189P THR* 5.0 3.8 - - + -
193P ILE* 3.1 34.5 - - + -
222P ILE* 6.0 0.9 - - + -
226P ASN* 5.4 0.4 - - - +
248P MLY 3.8 39.5 - - + -
249P PHE* 1.3 76.7 - - - +
251P ARG* 1.3 71.7 + - - +
252P ILE* 3.6 14.0 + - + +
263P ALA* 4.3 6.5 - - + -
264P ASP 3.2 17.3 - - - +
265P ILE* 4.3 16.6 - - + -
459P ILE 3.5 2.6 - - - +
460P GLY* 3.3 4.9 - - - -
461P VAL* 3.1 38.3 + - + +
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Residues in contact with ARG 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249P PHE* 4.0 21.5 - - + -
250P ILE* 1.3 78.8 - - - +
252P ILE* 1.3 62.0 + - - +
253P HIS* 3.1 45.0 + - + -
263P ALA* 3.0 22.7 - - - -
264P ASP* 3.0 41.8 + - + -
458P PHE* 3.7 35.8 - - + -
459P ILE 4.0 2.5 - - - -
663P ASN* 3.6 34.5 + - - +
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Residues in contact with ILE 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193P ILE* 3.9 33.0 - - + -
196P PHE* 4.6 19.7 - - + -
222P ILE* 5.0 6.7 - - + -
250P ILE* 4.3 12.3 - - + -
251P ARG* 1.3 72.3 - - - +
253P HIS* 1.3 62.0 + - - +
254P PHE* 3.3 24.4 - - + -
260P LEU* 3.2 35.4 - - + -
262P SER 3.4 4.9 - - - +
263P ALA* 4.6 6.7 - - + -
458P PHE* 3.0 3.5 - - - -
459P ILE 2.7 44.5 + - - +
461P VAL* 4.6 10.1 - - + -
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Residues in contact with HIS 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251P ARG* 3.1 66.7 + - + +
252P ILE* 1.3 71.1 - - - +
254P PHE* 1.3 63.6 + - - +
260P LEU* 4.4 0.3 - - - -
261P ALA* 2.9 24.8 + - - +
262P SER* 2.4 40.7 + - - +
263P ALA 4.3 0.2 + - - -
264P ASP* 3.6 10.2 + - - -
455P ARG* 4.2 32.6 + - + -
457P TYR 3.5 5.6 - - - +
458P PHE* 3.6 20.0 - + + +
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Residues in contact with PHE 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163P TYR* 4.1 11.9 - + - -
166P MET* 3.0 41.7 - - + -
196P PHE* 3.6 32.1 - + + -
200P ALA* 4.3 7.6 - - + -
252P ILE* 3.3 29.4 - - + -
253P HIS* 1.3 76.6 - - - +
255P GLY* 1.3 66.9 + - - +
258P GLY* 3.9 20.6 - - - +
259P LYS 4.2 0.9 - - - -
260P LEU* 3.7 30.5 - - + -
261P ALA* 4.2 0.7 - - - -
455P ARG* 3.8 3.3 - - - -
456P GLN 3.4 11.8 + - - -
457P TYR 2.7 18.9 + - - +
459P ILE* 3.3 25.1 - - + -
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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