Contacts of the strand formed by residues 97 - 101 (chain Q) 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 97 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Q ASP 3.0 4.3 + - - +
42Q VAL* 3.2 23.8 - - + -
43Q LEU 2.9 23.9 + - - -
95Q PRO* 3.8 1.6 - - - +
96Q LYS* 1.3 84.5 - - + +
98Q ILE* 1.3 77.5 + - - +
99Q VAL* 4.5 1.1 - - + -
133Q LYS* 3.3 14.1 - - + +
135Q ILE* 4.1 22.4 - - + -
213Q ILE* 4.2 7.0 - - + -
216Q LEU* 3.8 32.3 - - + +
217Q LEU* 3.8 17.9 - - + -
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Residues in contact with ILE 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q LEU* 3.2 25.6 - - + +
45Q VAL* 4.2 8.7 - - + -
90Q LEU* 4.1 13.2 - - + -
95Q PRO* 3.7 27.1 - - + -
97Q VAL* 1.3 79.0 - - - +
99Q VAL* 1.3 58.9 + - - +
100Q VAL* 4.2 8.5 - - + -
125Q ILE* 3.8 45.1 - - + -
129Q GLN* 4.5 7.0 - - + -
132Q ALA* 4.2 9.2 - - + +
133Q LYS 3.0 7.1 + - - +
134Q ILE* 3.3 9.9 - - + +
135Q ILE* 2.8 33.1 + - - +
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Residues in contact with VAL 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q VAL* 5.4 0.2 - - - +
43Q LEU 2.8 7.7 + - - +
44Q PHE* 3.4 45.8 - - + -
45Q VAL* 2.9 30.4 + - - +
50Q VAL* 5.5 0.9 - - + -
97Q VAL* 4.5 2.9 - - + -
98Q ILE* 1.3 73.8 - - - +
100Q VAL* 1.3 68.7 + - - +
101Q TRP* 5.0 5.2 - - + +
135Q ILE* 3.3 31.0 - - + +
137Q LEU* 4.7 9.6 - - + -
209Q LEU* 3.8 22.4 - - + -
213Q ILE* 4.2 5.6 - - + -
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Residues in contact with VAL 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Q VAL* 3.6 11.9 - - + +
98Q ILE* 4.2 4.3 - - + -
99Q VAL* 1.3 76.9 - - - +
101Q TRP* 1.3 65.3 + - - +
102Q VAL* 3.7 21.3 - - + +
118Q ILE* 4.6 10.5 - - + -
121Q ILE* 4.1 17.9 - - + -
122Q VAL* 5.3 1.6 - - + -
125Q ILE* 3.7 29.6 - - + -
134Q ILE* 4.3 13.0 - - + -
135Q ILE 2.7 12.3 + - - +
136Q VAL* 3.4 18.5 - - + +
137Q LEU* 2.9 26.9 + - - +
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Residues in contact with TRP 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q PHE* 6.2 0.2 - + - -
45Q VAL 3.1 8.1 + - - -
46Q GLY* 3.3 1.2 - - - -
47Q ASP* 3.0 31.1 + - - +
49Q MET* 3.5 44.6 - - + +
50Q VAL* 3.5 14.6 - - + -
53Q MET* 3.7 25.6 - - + -
99Q VAL* 5.1 3.6 - - + -
100Q VAL* 1.3 76.1 - - - +
102Q VAL* 1.3 63.7 - - - +
104Q THR* 5.9 1.2 - - - +
136Q VAL* 5.6 0.2 - - - -
137Q LEU* 3.0 53.2 - - + -
138Q GLY 3.5 13.4 + - - -
139Q LEU* 4.6 13.3 - - + +
140Q LEU* 3.4 37.6 - - + +
197Q LEU* 4.6 7.9 - - + -
202Q TYR* 4.5 1.1 - + - -
205Q ILE* 4.2 12.8 - - + -
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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