Contacts of the strand formed by residues 173 - 179 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162M ALA* 3.6 24.7 - - + +
165M PHE* 3.6 9.1 + - - +
166M MET* 3.6 14.1 - - - +
169M ASP* 5.2 0.5 - - - +
171M GLU* 2.9 31.4 + - - +
172M ASN* 1.3 78.6 + - - +
174M SER* 1.3 59.0 + - - +
458M PHE* 3.2 7.4 + - - +
459M ILE* 3.6 23.6 - - + -
460M GLY* 3.0 20.6 + - - -
667M THR* 3.0 16.1 + - - +
668M HIS* 2.6 39.5 + - - +
670M HIS* 3.2 25.7 + - + -
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Residues in contact with SER 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M GLN* 1.3 73.3 - - - +
175M ILE* 1.3 59.9 + - - +
176M LEU* 3.3 13.2 - - - +
249M PHE* 5.5 0.9 - - - -
458M PHE* 6.2 0.2 - - - -
460M GLY* 3.0 15.7 - - - +
462M LEU* 6.3 0.2 - - - -
490M PHE* 5.1 0.5 - - - -
664M LEU* 4.7 14.7 + - - +
667M THR* 2.9 25.7 - - - +
668M HIS 3.2 2.6 + - - -
669M PRO* 3.1 16.5 - - - +
670M HIS* 2.7 37.9 + - - +
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Residues in contact with ILE 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158M ILE* 4.0 21.8 - - + -
159M SER* 4.8 1.6 - - - -
162M ALA* 4.5 10.3 - - + -
174M SER* 1.3 80.0 - - - +
176M LEU* 1.3 66.0 + - - +
177M ILE* 3.5 27.1 - - + -
192M VAL* 4.7 10.3 - - + -
196M PHE* 4.2 18.4 - - + -
459M ILE* 4.2 22.9 - - + -
460M GLY 2.7 9.1 + - - +
461M VAL* 3.7 9.8 - - + +
462M LEU* 3.0 26.0 + - - +
670M HIS* 2.9 8.5 - - + +
672M VAL* 3.8 19.7 - - + -
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Residues in contact with LEU 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M SER* 3.3 24.2 - - - +
175M ILE* 1.3 79.1 - - - +
177M ILE* 1.4 61.5 + - - +
178M THR* 5.9 0.4 - - - +
462M LEU* 3.6 31.2 - - + -
487M LEU* 4.6 10.5 - - + -
490M PHE* 4.5 10.5 - - + -
664M LEU* 4.4 16.8 - - + -
669M PRO* 4.5 3.1 - - + -
670M HIS 2.7 28.8 + - - +
671M PHE* 4.2 21.1 - - + -
672M VAL 2.8 26.7 + - - +
673M ARG* 3.0 17.2 + - - +
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Residues in contact with ILE 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M ILE* 3.5 23.8 - - + -
176M LEU* 1.4 70.7 - - - +
178M THR* 1.3 71.1 + - - +
185M LYS* 3.6 23.5 - - + +
188M ASN* 4.8 3.8 - - + -
189M THR* 4.4 22.9 - - + +
192M VAL* 4.4 11.0 - - + -
461M VAL* 4.0 21.1 - - + -
462M LEU* 2.9 22.5 + - - +
463M ASP* 4.0 1.7 - - - -
464M ILE 3.7 13.2 + - - +
672M VAL* 3.3 24.7 - - + +
674M CYS* 3.5 26.7 - - - -
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Residues in contact with THR 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M LEU* 5.4 0.3 - - - +
177M ILE* 1.3 80.8 + - - +
179M GLY* 1.4 61.3 + - - +
185M LYS* 4.3 4.3 - - - -
462M LEU* 5.7 3.3 - - - +
464M ILE* 3.5 15.8 + - - +
465M ALA 4.2 2.4 + - - -
466M GLY* 4.6 10.5 - - - -
484M ASN* 4.0 14.4 + - - +
487M LEU* 5.4 4.3 - - - +
672M VAL 3.3 5.1 + - - -
673M ARG* 3.6 39.2 + - - +
674M CYS* 2.9 26.0 + - - +
697M CYS 5.8 1.1 - - - +
698M ASN* 4.8 12.2 + - - +
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Residues in contact with GLY 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178M THR* 1.4 78.6 - - - +
180M GLU* 1.3 63.4 + - - -
183M ALA* 4.1 4.7 - - - -
185M LYS* 2.9 25.7 - - - +
464M ILE 4.3 1.2 + - - -
465M ALA* 4.2 2.1 - - - +
466M GLY* 3.8 17.9 + - - +
674M CYS* 3.7 14.8 - - - -
698M ASN* 5.4 3.8 - - - -
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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