Contacts of the strand formed by residues 42 - 46 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PRO* 3.6 7.0 - - - +
41A ASP* 1.3 88.1 - - + +
43A LEU* 1.3 64.0 + - - +
44A PHE* 3.7 27.6 - - + -
66A LEU* 3.8 36.8 - - + +
67A HIS 3.2 1.4 + - - -
68A ALA* 3.1 11.7 - - + -
69A LEU 3.0 23.3 + - - -
95A PRO* 4.4 0.4 - - - -
97A VAL* 3.3 13.2 - - + +
99A VAL* 4.4 9.2 - - + -
213A ILE* 4.4 19.3 - - + -
217A LEU* 4.5 7.2 - - + -
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Residues in contact with LEU 43 (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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40A PRO* 5.4 2.0 - - + -
42A VAL* 1.3 75.2 - - - +
44A PHE* 1.3 76.3 + - - +
45A VAL* 3.3 26.2 - - + -
69A LEU* 3.1 28.9 - - + +
71A PHE* 4.1 22.4 - - + -
90A LEU* 4.7 12.6 - - + -
93A ILE* 4.6 17.9 - - + -
95A PRO* 4.0 18.6 - - + -
97A VAL 2.9 9.6 + - - +
98A ILE* 3.2 19.0 - - + +
99A VAL 2.7 31.2 + - - -
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Residues in contact with PHE 44 (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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42A VAL* 3.7 22.4 - - + -
43A LEU* 1.3 73.5 - - - +
45A VAL* 1.3 64.0 + - - +
50A VAL* 3.9 23.3 - - + -
53A MET* 3.8 25.1 - - + -
59A TRP* 3.5 22.9 - + - -
63A PHE* 3.9 34.5 - + - -
68A ALA* 4.3 5.4 - - + -
69A LEU 2.8 16.4 + - - +
70A ASN* 4.0 4.7 - - - +
71A PHE 2.7 28.6 + - - -
99A VAL* 3.6 31.0 - - + -
101A TRP* 6.1 2.5 - + - -
137A LEU* 6.2 0.2 - - + -
209A LEU* 3.8 14.8 - - + -
213A ILE* 4.3 2.5 - - + -
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Residues in contact with VAL 45 (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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43A LEU* 3.3 30.1 - - + +
44A PHE* 1.3 76.7 - - - +
46A GLY* 1.3 59.5 + - - +
50A VAL* 3.4 8.2 - - - +
71A PHE* 4.1 16.6 - - + +
81A VAL* 4.8 14.4 - - + -
84A ARG* 5.3 2.7 - - - +
85A LEU* 4.5 17.9 - - + -
98A ILE* 4.7 4.5 - - + -
99A VAL 2.9 9.4 + - - +
100A VAL* 3.6 30.1 - - + -
101A TRP 3.0 19.4 + - - -
125A ILE* 4.9 6.3 - - + -
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Residues in contact with GLY 46 (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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45A VAL* 1.3 79.1 - - - +
47A ASP* 1.3 61.8 + - - -
50A VAL* 3.7 4.4 - - - +
71A PHE 4.0 4.9 + - - -
72A GLY* 3.3 2.3 - - - -
73A ILE 3.1 21.8 + - - +
76A ASP* 4.4 0.3 - - - +
81A VAL* 4.0 9.9 - - - +
84A ARG* 3.4 9.6 + - - +
101A TRP 3.2 11.2 - - - -
102A VAL* 3.6 15.7 - - - -
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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