Contacts of the strand formed by residues 173 - 179 (chain G) 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 GLN 173 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162G ALA* 3.6 24.5 - - + +
165G PHE* 3.6 9.5 + - - +
166G MET* 3.6 14.1 - - - +
169G ASP* 5.2 0.5 - - - +
171G GLU* 2.9 31.5 + - - +
172G ASN* 1.3 79.4 + - - +
174G SER* 1.3 57.2 + - - +
458G PHE* 3.2 7.1 + - - +
459G ILE* 3.6 23.4 - - + -
460G GLY* 3.0 21.1 + - - -
667G THR* 3.0 17.7 + - - +
668G HIS* 2.6 39.0 + - - +
670G HIS* 3.2 25.4 + - + -
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Residues in contact with SER 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G GLN* 1.3 74.1 - - - +
175G ILE* 1.3 59.4 + - - +
176G LEU* 3.3 13.1 - - - +
249G PHE* 5.5 1.1 - - - -
459G ILE 5.0 0.2 - - - -
460G GLY* 3.0 15.9 - - - +
462G LEU* 6.3 0.2 - - - -
490G PHE* 5.1 0.5 - - - -
664G LEU* 4.7 14.9 + - - +
667G THR* 2.9 25.5 - - - +
668G HIS 3.2 2.8 + - - -
669G PRO* 3.1 16.3 - - - +
670G HIS* 2.7 38.7 + - - +
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Residues in contact with ILE 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G ILE* 4.0 22.0 - - + -
159G SER* 4.8 1.3 - - - -
162G ALA* 4.5 10.8 - - + -
174G SER* 1.3 79.3 - - - +
176G LEU* 1.3 64.8 + - - +
177G ILE* 3.5 26.2 - - + -
192G VAL* 4.7 10.3 - - + -
196G PHE* 4.2 18.4 - - + -
459G ILE* 4.2 22.4 - - + -
460G GLY 2.7 9.5 + - - +
461G VAL* 4.3 11.6 - - + +
462G LEU* 3.0 26.5 + - - +
670G HIS* 2.9 7.6 - - + +
672G VAL* 3.8 19.5 - - + -
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Residues in contact with LEU 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G SER* 3.3 23.8 - - - +
175G ILE* 1.3 78.5 - - - +
177G ILE* 1.4 61.8 + - - +
178G THR* 5.9 0.7 - - - +
462G LEU* 3.6 31.9 - - + -
487G LEU* 4.6 11.4 - - + -
490G PHE* 4.5 10.3 - - + -
664G LEU* 4.4 16.6 - - + -
669G PRO* 4.5 3.4 - - + -
670G HIS 2.7 29.0 + - - +
671G PHE* 4.1 22.4 - - + -
672G VAL 2.8 26.3 + - - +
673G ARG* 3.0 17.9 + - - +
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Residues in contact with ILE 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G ILE* 6.2 0.2 - - + -
175G ILE* 3.5 24.0 - - + -
176G LEU* 1.4 69.7 - - - +
178G THR* 1.3 70.4 + - - +
185G LYS* 3.6 23.1 - - + +
188G ASN* 4.8 3.8 - - + -
189G THR* 4.4 22.9 - - + +
192G VAL* 4.4 9.9 - - + -
461G VAL* 4.0 21.3 - - + -
462G LEU* 2.9 21.6 + - - +
463G ASP* 4.0 2.3 - - - -
464G ILE 3.7 12.6 + - - +
672G VAL* 3.4 23.8 - - + -
674G CYS* 3.5 27.4 - - - -
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Residues in contact with THR 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G LEU* 5.1 0.6 - - - +
177G ILE* 1.3 81.7 + - - +
179G GLY* 1.4 62.1 + - - +
185G LYS* 4.3 3.4 - - - -
462G LEU* 5.7 2.8 - - - +
464G ILE* 3.5 17.7 + - - +
465G ALA 4.2 2.4 + - - -
466G GLY* 4.6 11.2 - - - -
484G ASN* 4.0 14.9 + - - +
487G LEU* 5.4 3.8 - - - +
672G VAL 3.3 4.6 + - - -
673G ARG* 3.6 40.5 + - - +
674G CYS* 2.9 26.0 + - - +
697G CYS 5.8 1.3 - - - +
698G ASN* 4.8 11.3 + - - +
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Residues in contact with GLY 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178G THR* 1.4 78.9 + - - +
180G GLU* 1.3 62.9 + - - -
183G ALA* 4.1 4.3 - - - -
185G LYS* 2.9 26.8 - - - +
464G ILE 4.3 1.2 + - - -
465G ALA* 4.2 2.1 - - - +
466G GLY* 3.8 18.4 + - - +
674G CYS 3.7 14.8 - - - -
698G ASN* 5.4 4.3 - - - -
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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