Contacts of the strand formed by residues 42 - 46 (chain M) in PDB entry 1VYH
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 VAL 42 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40M PRO* 3.6 7.0 - - - +
41M ASP* 1.3 86.6 - - + +
43M LEU* 1.3 64.9 + - - +
44M PHE* 3.5 26.5 - - + -
63M PHE* 5.9 0.4 - - + -
66M LEU* 3.9 35.7 - - + +
67M HIS 3.2 1.4 + - - -
68M ALA* 3.2 10.1 - - + -
69M LEU 2.9 25.3 + - - -
95M PRO* 4.5 0.7 - - - -
97M VAL* 3.2 14.6 - - + +
99M VAL* 4.8 1.6 - - + -
213M ILE* 3.9 28.7 - - + -
217M LEU* 4.4 6.5 - - + -
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Residues in contact with LEU 43 (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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40M PRO* 5.5 2.2 - - + -
42M VAL* 1.3 75.0 - - - +
44M PHE* 1.3 66.6 + - - +
45M VAL* 3.6 23.1 - - + -
69M LEU* 3.6 23.8 - - + +
71M PHE* 3.8 30.7 - - + -
85M LEU* 5.3 0.7 - - + -
89M GLU 4.6 1.3 - - - +
90M LEU* 4.6 13.0 - - + -
93M ILE* 4.1 25.8 - - + -
95M PRO* 4.0 15.3 - - + -
97M VAL 2.9 8.1 + - - -
98M ILE* 3.2 24.6 - - + +
99M VAL 2.8 25.9 + - - -
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Residues in contact with PHE 44 (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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42M VAL* 3.5 23.6 - - + -
43M LEU* 1.3 78.0 - - - +
45M VAL* 1.3 58.9 + - - +
50M VAL* 3.6 21.7 - - + +
53M MET* 3.7 28.3 - - + -
59M TRP* 3.8 21.1 - + + -
63M PHE* 3.7 28.7 - + - -
68M ALA* 4.2 8.5 - - + -
69M LEU 2.8 20.3 + - - +
70M ASN* 4.4 3.4 - - - -
71M PHE* 2.7 34.7 + - - +
99M VAL* 3.5 22.2 - - + +
209M LEU* 3.8 16.6 - - + -
213M ILE* 4.2 10.5 - - + -
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Residues in contact with VAL 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M LEU* 3.6 23.6 - - + -
44M PHE* 1.3 78.6 - - - +
46M GLY* 1.3 59.0 + - - +
50M VAL* 3.4 9.0 - - - +
71M PHE* 3.7 22.9 - - + +
81M VAL* 5.0 8.3 - - + -
84M ARG* 5.0 2.2 - - - +
85M LEU* 4.2 29.2 - - + -
89M GLU* 4.9 2.2 - - - +
98M ILE* 4.5 9.0 - - + -
99M VAL 2.9 17.7 + - - +
100M VAL* 3.8 21.3 - - + -
101M TRP 3.0 22.3 + - - -
102M VAL* 5.0 0.2 - - - -
125M ILE* 4.9 0.9 - - + -
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Residues in contact with GLY 46 (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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45M VAL* 1.3 79.0 - - - +
47M ASP* 1.3 61.7 + - - -
50M VAL* 3.7 4.0 - - - +
71M PHE 4.0 4.4 + - - -
72M GLY* 3.2 2.3 - - - -
73M ILE 3.0 11.8 + - - -
81M VAL* 4.0 10.5 - - - +
84M ARG* 3.0 23.9 + - - +
101M TRP 3.3 11.4 - - - -
102M VAL* 3.9 12.6 - - - -
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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