Contacts of the strand formed by residues 33 - 38 (chain A) in PDB entry 2VL3
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 LYS 33 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 1.3 75.7 - - - +
34A GLY* 1.3 60.3 - - - +
65A LYS 3.0 26.3 + - - +
66A GLY* 3.5 19.9 + - - +
67A VAL* 4.0 8.5 - - + -
68A GLN* 2.9 31.9 + - - +
69A VAL* 3.7 4.3 + - - +
131A VAL* 4.6 8.5 - - + -
132A VAL 3.5 8.7 - - - +
133A GLN* 4.1 29.8 - - + +
161A LEU* 4.0 32.2 + - + +
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Residues in contact with GLY 34 (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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29A PHE* 3.8 17.4 - - - -
32A LYS 4.0 1.0 + - - -
33A LYS* 1.3 76.3 - - - +
35A VAL* 1.3 66.4 + - - +
67A VAL* 4.1 2.0 - - - -
69A VAL* 3.2 15.0 - - - -
131A VAL* 3.5 8.0 - - - +
132A VAL 2.8 33.9 + - - +
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.9 5.3 - - - -
34A GLY* 1.3 78.8 - - - +
36A LEU* 1.3 69.9 + - - +
37A PHE* 4.6 1.1 - - + -
55A PHE* 3.9 28.0 - - + -
62A LEU* 5.1 3.6 - - + -
67A VAL* 4.0 21.5 - - + -
69A VAL 2.8 8.6 + - - +
70A VAL* 3.3 13.4 - - + -
71A ALA 3.0 25.1 + - - -
130A MET 3.1 13.7 - - - +
131A VAL* 4.7 0.7 - - + -
157A ILE* 4.0 29.8 - - + -
161A LEU* 4.6 4.7 - - + -
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Residues in contact with LEU 36 (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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9A ILE* 4.6 6.3 - - + -
25A LEU* 4.6 10.8 - - + -
29A PHE* 3.8 23.0 - - + -
34A GLY 4.3 0.4 - - - -
35A VAL* 1.3 75.5 - - - +
37A PHE* 1.3 60.8 + - - +
71A ALA* 3.5 29.6 - - + +
73A LEU* 4.2 21.8 - - + -
97A LEU* 5.0 0.4 - - + -
104A PHE* 3.7 33.9 - - + -
128A PHE* 3.9 17.0 - - + -
129A SER* 3.4 1.2 - - - -
130A MET* 2.8 53.0 + - + +
132A VAL* 4.6 2.6 - - + +
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Residues in contact with PHE 37 (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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35A VAL* 4.6 0.7 - - + -
36A LEU* 1.3 77.1 - - - +
38A GLY* 1.3 57.3 + - - +
39A VAL* 4.2 7.9 - - + -
51A HIS* 3.7 27.8 - + + -
52A LEU* 4.0 15.3 - - + -
55A PHE* 3.4 53.2 - + + -
70A VAL* 4.0 13.0 - - + -
71A ALA 3.0 20.6 + - - -
72A CYS* 3.3 36.1 - - + -
73A LEU* 2.9 26.7 + - - +
94A VAL* 4.2 2.5 - - + -
128A PHE* 3.1 20.9 - - - +
129A SER* 3.9 12.6 - - - -
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Residues in contact with GLY 38 (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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37A PHE* 1.3 74.5 - - - +
39A VAL* 1.3 67.7 + - - +
51A HIS* 3.8 1.4 - - - -
73A LEU 3.4 8.7 - - - -
125A LEU* 4.5 1.1 - - - -
126A LYS 4.1 6.3 - - - -
127A ARG* 3.3 9.9 - - - +
128A PHE* 2.7 54.9 + - - +
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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