Contacts of the helix formed by residues 34 - 46 (chain A) in PDB entry 1V1A
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 GLY 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLU 3.7 20.0 - - - -
11A LEU* 4.0 6.3 - - - +
33A GLY* 1.3 71.5 - - - -
35A ALA* 1.3 56.0 + - - -
36A GLU* 3.3 2.7 - - - -
37A VAL* 3.0 5.4 + - - -
38A ASN* 2.7 35.5 + - - -
1302A KDG 3.1 25.2 + - - +
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Residues in contact with ALA 35 (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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34A GLY* 1.3 71.3 - - - +
36A GLU* 1.3 70.9 + - - +
38A ASN 3.2 0.7 + - - -
39A VAL* 3.0 32.1 + - - +
130A HIS* 5.8 0.2 - - - -
132A SER* 4.0 7.4 - - - +
134A ILE* 3.4 31.2 - - + -
165A ASN* 4.0 2.0 - - - +
251A ASP* 3.2 30.8 - - - +
1302A KDG 2.6 12.7 + - - +
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Residues in contact with GLU 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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6A THR* 3.4 8.5 + - - -
7A ALA 3.0 33.0 - - - +
8A GLY* 3.5 13.5 - - - -
9A GLU 3.8 10.1 + - - +
35A ALA* 1.3 80.2 + - - +
37A VAL* 1.3 59.6 + - - +
39A VAL* 3.7 7.5 - - - +
40A ALA* 2.9 29.1 + - - +
52A PHE* 3.7 18.2 - - + -
130A HIS* 4.6 9.4 - - + -
131A LEU 4.6 0.7 - - - -
132A SER* 2.8 38.3 + - - +
134A ILE* 4.5 3.3 - - - +
135A THR* 3.0 14.7 + - - -
1302A KDG 5.2 0.2 - - - +
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Residues in contact with VAL 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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9A GLU 4.8 0.4 - - - +
10A PRO* 3.8 21.1 - - + -
32A VAL* 4.2 16.2 - - + -
33A GLY 3.1 28.9 - - - +
34A GLY* 3.0 3.5 + - - +
36A GLU* 1.3 74.2 - - - +
38A ASN* 1.3 67.3 + - - +
40A ALA* 3.2 5.4 + - - +
41A VAL* 2.9 35.8 + - + +
52A PHE* 3.6 31.4 - - + -
65A VAL* 5.3 0.9 - - + -
69A LEU* 4.0 22.7 - - + -
288A HIS* 4.6 3.1 - - + -
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Residues in contact with ASN 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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33A GLY* 3.6 6.8 - - - -
34A GLY 2.7 17.1 + - - +
35A ALA 3.4 6.5 - - - +
37A VAL* 1.3 74.2 - - - +
39A VAL* 1.3 62.7 + - - +
41A VAL* 3.3 2.1 + - - +
42A ALA* 3.1 24.5 + - - +
248A GLY* 4.2 1.2 - - - +
251A ASP* 2.8 30.6 + - + +
252A ALA* 5.4 0.6 - - - +
287A ASP* 3.5 24.8 + - - +
288A HIS* 2.9 37.6 + - + +
1302A KDG 2.8 27.3 + - - -
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Residues in contact with VAL 39 (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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6A THR* 4.0 11.0 - - + -
35A ALA* 3.0 20.4 + - + +
36A GLU 3.7 7.4 - - - +
38A ASN* 1.3 75.4 - - - +
40A ALA* 1.3 63.2 + - - +
42A ALA* 3.4 2.4 + - - +
43A LEU* 3.1 32.9 + - + +
130A HIS* 3.6 37.0 - - + +
163A ASP* 6.1 0.2 - - - +
251A ASP* 3.6 26.0 - - + +
254A ALA* 4.5 4.5 - - + -
255A ALA* 3.9 22.9 - - + -
258A LEU* 4.4 7.0 - - + -
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Residues in contact with ALA 40 (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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6A THR* 3.2 26.0 - - - +
36A GLU 2.9 11.9 + - - +
37A VAL* 3.2 9.2 + - + +
39A VAL* 1.3 74.4 - - - +
41A VAL* 1.3 64.9 + - - +
43A LEU* 3.4 0.7 + - - -
44A ALA* 2.9 18.9 + - - +
50A VAL* 3.2 28.6 - - + +
52A PHE* 4.4 2.5 - - + -
69A LEU* 5.7 0.7 - - + -
74A VAL* 4.0 18.6 - - + -
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Residues in contact with VAL 41 (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 VAL* 2.9 32.3 + - + +
38A ASN 3.9 1.3 - - - +
40A ALA* 1.3 69.3 - - - +
42A ALA* 1.3 69.2 + - - +
44A ALA* 2.7 9.8 + - - +
45A ARG* 2.7 49.9 + - - +
68A ARG* 5.0 3.6 - - + -
69A LEU* 5.1 2.9 - - + -
72A GLU* 3.4 28.5 - - + -
74A VAL* 4.3 7.2 - - + -
288A HIS* 3.4 38.1 - - + +
291A ALA* 5.5 0.2 - - + -
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Residues in contact with ALA 42 (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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38A ASN 3.1 10.9 + - - +
39A VAL* 3.5 3.4 - - - +
41A VAL* 1.3 80.5 - - - +
43A LEU* 1.3 63.0 + - - +
45A ARG* 3.1 4.3 + - - +
46A LEU* 3.0 27.7 + - - +
252A ALA* 4.8 7.0 - - - -
255A ALA* 3.5 26.0 - - + -
277A LEU* 4.4 11.9 - - + -
288A HIS* 5.4 0.6 - - + -
291A ALA* 4.3 24.0 - - + +
292A PRO 4.7 0.3 - - - +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A VAL* 3.6 39.7 - - + -
39A VAL* 3.1 31.2 + - + +
42A ALA* 1.3 78.5 - - - +
44A ALA* 1.3 58.6 + - - +
46A LEU* 2.9 21.1 + - + +
48A VAL* 3.2 32.8 + - + -
50A VAL* 3.7 17.9 - - + -
255A ALA* 3.0 32.8 - - + +
258A LEU* 4.6 6.1 - - + -
259A ALA* 3.9 21.5 - - + +
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Residues in contact with ALA 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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40A ALA 2.9 14.3 + - - +
41A VAL* 2.7 19.0 + - - +
43A LEU* 1.3 73.5 - - - +
45A ARG* 1.3 57.8 + - - +
46A LEU 3.4 0.5 + - - -
47A GLY* 3.4 10.2 + - - -
48A VAL 3.9 5.2 - - - +
50A VAL* 3.5 10.0 - - + +
72A GLU* 4.1 25.1 - - + +
73A GLY 4.6 2.7 - - - +
74A VAL* 3.9 21.8 - - + +
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Residues in contact with ARG 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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41A VAL* 2.7 23.7 + - - +
42A ALA 3.6 8.1 - - - +
44A ALA* 1.3 72.4 - - - +
46A LEU* 1.3 60.7 + - - +
47A GLY 3.4 0.6 + - - -
68A ARG* 4.4 5.1 - - - +
72A GLU* 3.2 39.4 + - - +
288A HIS* 3.7 29.0 + - - -
289A GLU* 3.2 30.9 + - - -
291A ALA* 3.0 31.9 + - - +
292A PRO 3.6 10.1 - - - +
293A TYR* 3.4 48.0 + - + +
294A ARG* 3.0 23.7 + - - +
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Residues in contact with LEU 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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42A ALA* 3.0 20.2 - - + +
43A LEU* 2.9 12.8 + - - +
45A ARG* 1.3 78.3 - - - +
47A GLY* 1.3 55.1 + - - +
48A VAL* 3.3 6.1 - - + +
255A ALA 4.5 6.3 - - - +
256A GLY* 4.7 1.3 - - - -
259A ALA* 4.2 18.8 - - + -
263A TRP* 3.3 25.7 - - + -
273A LEU* 6.0 1.1 - - + -
277A LEU* 4.0 27.8 - - + -
292A PRO 3.6 20.0 - - - +
294A ARG* 3.1 25.5 - - - +
297A LEU* 3.6 36.6 - - + -
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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