Contacts of the strand formed by residues 28 - 32 (chain A) in PDB entry 2VL7
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 THR 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLY 3.9 1.8 + - - -
27A LYS* 1.3 70.5 - - - +
29A LEU* 1.3 62.9 + - - +
30A LEU* 4.5 6.3 - - + -
316A LEU* 5.9 1.8 - - + -
322A LYS* 3.7 40.0 + - + +
324A LEU* 3.5 31.4 - - + -
335A LEU* 4.7 10.3 - - + -
336A THR 4.3 8.8 + - - -
337A ASN* 2.9 15.0 + - - +
338A SER* 3.2 7.9 - - - -
339A TYR 2.9 23.8 + - - -
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Residues in contact with LEU 29 (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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19A ALA* 3.7 25.4 - - + -
22A ALA* 4.1 19.1 - - + -
23A LEU* 3.9 18.6 - - + -
27A LYS 3.7 2.6 + - - -
28A THR* 1.3 71.6 - - - +
30A LEU* 1.3 64.1 + - - +
31A LEU* 4.9 6.5 - - + +
42A PHE* 4.9 4.7 - - + -
46A LEU* 4.2 8.3 - - + -
322A LYS 3.1 9.6 + - - +
323A VAL* 3.3 24.9 - - + -
324A LEU 2.8 32.1 + - - +
339A TYR* 3.4 15.5 - - + +
341A ILE* 3.8 31.0 - - + -
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Residues in contact with LEU 30 (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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28A THR* 4.5 6.3 - - + -
29A LEU* 1.3 77.4 - - - +
31A LEU* 1.3 57.0 + - - +
324A LEU* 3.3 38.4 - - + +
329A LEU* 3.6 14.8 - - + -
333A LEU* 4.0 26.2 - - + +
334A THR* 5.6 0.2 - - - -
335A LEU* 4.6 10.1 - - + +
338A SER* 4.1 28.3 - - - +
339A TYR 2.8 10.6 + - - +
340A LYS* 3.2 30.2 - - + +
341A ILE* 2.7 33.3 + - - +
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Residues in contact with LEU 31 (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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11A TRP* 4.4 15.0 - - + -
29A LEU* 4.9 4.7 - - + -
30A LEU* 1.3 73.2 - - - +
32A ASN* 1.3 63.4 + - - +
33A ALA* 4.8 1.8 - - + -
39A LYS* 4.6 8.7 - - + +
42A PHE* 3.9 31.6 - - + -
43A VAL* 4.4 5.2 - - + -
323A VAL* 4.5 8.5 - - + -
324A LEU 2.9 9.0 + - - +
325A MET* 3.2 30.5 - - + -
326A SER 3.1 26.2 + - - +
329A LEU* 3.3 7.4 - - - +
341A ILE* 3.5 32.8 - - + +
343A VAL* 4.2 16.2 - - + -
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Residues in contact with ASN 32 (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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31A LEU* 1.3 71.8 - - - +
33A ALA* 1.3 70.0 + - - +
34A LYS* 4.2 3.6 - - - +
326A SER 3.4 2.9 - - - -
327A GLY 3.9 9.6 + - - +
328A THR* 3.6 5.0 - - - -
329A LEU* 2.7 47.4 + - + +
340A LYS* 5.7 0.4 - - + -
341A ILE 3.0 12.0 + - - +
342A VAL* 4.3 24.6 - - + +
343A VAL* 2.9 35.9 + - - +
499A LYS* 5.9 2.0 + - - +
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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