Contacts of the helix formed by residues 24 - 36 (chain B) in PDB entry 2VDE
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 ASN 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLU* 1.3 74.1 - - - +
25B LEU* 1.3 57.2 + - - +
26B MET* 4.0 1.9 - - - +
27B GLN* 3.0 44.3 + - - +
28B VAL* 2.8 35.0 + - - +
135B TYR* 3.9 10.8 - - - +
216B ALA* 4.0 15.2 - - + +
438B ASN* 2.9 36.8 - - - +
441B LEU* 4.7 0.7 - - + -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ASN* 1.3 75.3 - - - +
26B MET* 1.3 57.2 + - - +
28B VAL* 4.5 0.9 - - + -
29B TYR* 2.8 31.6 + - - +
131B THR* 4.5 6.7 - - + +
132B ALA* 4.0 17.0 - - + +
135B TYR* 3.8 40.4 + - + -
136B PHE* 3.9 28.5 - - + -
434B LEU* 3.8 33.4 - - + +
437B LEU* 4.1 18.6 - - + -
438B ASN* 3.3 8.2 + - + +
441B LEU* 4.1 13.2 - - + +
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN* 4.0 2.0 - - - +
25B LEU* 1.3 72.5 - - - +
27B GLN* 1.3 58.6 + - + +
29B TYR* 3.7 4.2 - - - +
30B GLN* 2.8 65.4 + - - +
431B GLU* 3.8 18.2 - - + +
434B LEU* 3.7 15.3 - - - +
435B LEU* 3.4 51.4 - - + -
438B ASN* 3.0 32.8 + - + +
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Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU* 3.3 24.7 - - + +
24B ASN* 3.0 48.6 + - - +
26B MET* 1.3 78.1 - - + +
28B VAL* 1.3 62.2 + - - +
30B GLN* 4.1 10.2 - - - +
31B GLN* 3.3 33.5 + - - +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU* 4.1 6.1 - - + -
24B ASN 2.8 25.2 + - - +
25B LEU* 4.0 4.5 - - - +
27B GLN* 1.3 68.8 - - - +
29B TYR* 1.3 65.5 + - - +
31B GLN* 3.4 1.8 + - - +
32B ALA* 3.1 16.8 + - - +
131B THR* 4.2 9.6 - - + -
135B TYR* 4.5 8.1 - - + -
204B LEU* 4.0 13.9 - - + -
208B THR* 3.5 26.4 - - - +
212B TYR* 3.6 37.2 - - + -
215B LEU* 4.0 22.0 - - + -
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Residues in contact with TYR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU 2.8 24.3 + - - +
26B MET* 3.7 3.6 - - - +
28B VAL* 1.3 74.5 - - - +
30B GLN* 1.3 69.8 + - + +
32B ALA* 2.9 5.9 + - - +
33B ARG* 2.9 44.2 + - + +
124B GLN* 4.7 2.1 + - - +
127B LEU* 4.4 17.0 - - + +
128B ILE* 3.2 48.3 - - + +
131B THR* 3.9 28.7 - - + -
431B GLU* 4.2 28.1 - - + +
434B LEU* 3.6 25.8 - - + -
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Residues in contact with GLN 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B MET* 2.8 59.2 + - - +
27B GLN* 4.2 8.0 - - - +
29B TYR* 1.3 79.9 - - + +
31B GLN* 1.3 61.1 + - - +
33B ARG* 3.3 30.1 + - - +
34B LEU* 3.6 28.8 + - - +
431B GLU* 3.7 12.8 - - - +
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Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU* 4.5 10.4 + - - +
27B GLN* 3.3 22.4 + - - +
28B VAL 3.7 4.7 - - - +
29B TYR 3.2 0.4 - - - -
30B GLN* 1.3 76.5 - - + +
32B ALA* 1.3 62.0 + - - +
34B LEU* 3.9 6.6 + - - +
35B SER* 3.6 22.0 + - - -
208B THR* 3.9 4.2 - - - +
210B ASN* 3.2 28.2 + - - +
212B TYR* 2.9 35.0 + - - +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL 3.1 12.5 + - - +
29B TYR* 2.9 10.4 + - - +
31B GLN* 1.3 76.3 - - - +
33B ARG* 1.3 59.3 + - - +
36B ASN* 2.7 37.2 + - - +
127B LEU* 4.4 6.5 - - + -
131B THR* 4.3 17.7 - - + +
207B ILE* 4.4 8.3 - - + +
208B THR* 3.9 29.6 - - + +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 2.9 34.1 + - + +
30B GLN* 3.3 27.7 + - - +
31B GLN 3.4 0.2 - - - -
32B ALA* 1.3 77.3 - - - +
34B LEU* 1.3 87.7 + - - +
36B ASN 4.3 2.3 + - - -
39B LEU* 4.4 21.7 - - + +
40B ARG* 4.7 5.7 - - - +
127B LEU* 4.1 11.1 - - + +
431B GLU* 3.2 27.7 + - - -
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLN 3.6 12.0 + - - +
31B GLN* 4.0 9.9 - - - +
33B ARG* 1.3 108.6 - - - +
35B SER* 1.3 57.8 + - - +
40B ARG* 2.9 32.3 + - - +
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A GLU* 4.3 1.0 - - - +
339A GLU* 5.1 2.8 - - - +
343A ARG* 2.8 34.4 + - - -
31B GLN 3.6 12.7 + - - -
32B ALA 3.3 2.0 + - - -
34B LEU* 1.3 81.8 - - - +
36B ASN* 1.3 67.6 + - - +
37B PRO* 3.0 9.3 - - - +
40B ARG* 4.0 14.1 + - - +
208B THR 4.0 3.6 - - - -
209B GLY* 5.2 0.7 - - - -
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Residues in contact with ASN 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ARG* 3.9 4.2 - - - +
32B ALA 2.7 23.9 + - - +
33B ARG 4.3 1.3 + - - +
34B LEU 3.9 0.4 - - - -
35B SER* 1.3 67.9 - - - +
37B PRO* 1.3 66.6 - - - +
38B GLU* 3.3 28.0 + - - +
39B LEU* 3.0 36.7 + - + +
40B ARG* 3.1 21.0 + - - +
127B LEU* 3.5 33.4 - - + +
207B ILE* 3.0 30.4 + - - +
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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