Contacts of the helix formed by residues 35 - 47 (chain C) in PDB entry 1DVM
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 SER 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C PHE* 1.3 81.1 - - - +
36C PRO* 1.3 56.6 - - - +
37C TYR* 3.2 1.4 - - - +
38C GLY 2.8 26.0 + - - -
39C VAL* 3.2 1.9 + - - +
169C LEU* 3.0 38.4 - - - +
322C GLN* 2.9 24.6 + - - -
324C VAL* 3.7 7.0 - - - -
371C LEU 2.7 21.1 + - - -
372C PHE* 3.9 3.4 - - - -
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Residues in contact with PRO 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA 4.3 2.0 - - - -
13C SER* 4.0 2.2 - - - +
16C GLY* 3.5 37.5 - - - +
17C VAL 4.0 1.6 - - - +
20C PHE* 4.6 0.7 - - + -
34C PHE* 3.6 17.9 - - + +
35C SER* 1.3 85.0 - - - +
37C TYR* 1.3 60.2 + - - +
39C VAL* 3.1 17.8 - - - +
40C ALA* 3.2 12.0 + - - +
370C VAL* 3.3 35.9 - - + +
371C LEU 4.0 0.7 - - - +
372C PHE 4.1 0.4 - - - -
373C MET* 3.9 28.3 - - + +
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Residues in contact with TYR 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 4.5 13.9 - - + -
13C SER* 5.4 0.7 - - - +
35C SER 3.2 0.2 - - - -
36C PRO* 1.3 78.8 - - - +
38C GLY* 1.3 61.6 + - - +
40C ALA* 3.6 4.2 + - - +
41C SER* 2.8 42.7 + - - -
75C LEU* 4.4 8.4 + - + +
78C LEU* 3.7 23.6 - - + -
79C TYR* 3.5 40.9 + + - +
82C LEU* 3.7 20.2 - - + -
93C THR* 5.5 8.5 - - + -
169C LEU* 5.1 9.0 - - + -
369C THR* 3.7 23.3 - - + -
370C VAL* 3.4 15.4 + - - +
371C LEU* 3.8 23.6 - - + +
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Residues in contact with GLY 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER* 2.8 17.3 + - - -
37C TYR* 1.3 78.2 - - - +
39C VAL* 1.3 65.4 + - - -
40C ALA 3.0 0.9 - - - -
41C SER* 2.8 17.4 + - - -
42C VAL* 3.0 15.1 + - - +
167C ASN* 3.1 28.0 + - - -
169C LEU* 4.7 3.6 - - - -
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 4.6 2.0 - - + -
16C GLY* 3.8 13.2 - - - -
19C VAL* 4.2 13.7 - - + -
34C PHE* 3.7 31.0 - - + -
35C SER 3.2 3.8 + - - -
36C PRO 3.1 14.4 - - - +
38C GLY* 1.3 71.6 - - - +
40C ALA* 1.3 60.8 + - - +
42C VAL* 3.2 7.6 - - - +
43C LEU* 3.1 45.8 + - + +
167C ASN* 4.3 0.4 - - - -
286C LEU* 3.9 34.5 - - + -
290C LEU* 4.4 7.9 - - + -
322C GLN* 3.3 9.1 - - - +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 3.3 38.4 - - + +
15C PHE* 3.9 20.2 - - + -
36C PRO 3.2 15.5 + - - +
37C TYR 3.7 4.0 - - - +
38C GLY 3.0 0.6 - - - -
39C VAL* 1.3 79.9 - - - +
41C SER* 1.3 63.1 + - - +
44C ALA* 3.1 25.3 + - - +
62C MET* 3.4 8.0 - - + +
75C LEU* 5.8 1.1 - - - +
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Residues in contact with SER 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 5.5 0.4 - - - +
37C TYR* 2.8 41.4 + - - -
38C GLY* 2.8 8.2 + - - -
40C ALA* 1.3 78.1 - - - +
42C VAL* 1.3 60.0 + - - -
44C ALA* 3.4 8.0 - - - +
45C MET* 3.3 29.7 + - - +
75C LEU* 5.5 8.5 - - - +
79C TYR* 5.7 2.1 - - - -
95C ASP* 3.5 19.7 + - - -
117C PHE* 4.7 1.6 - - - -
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Residues in contact with VAL 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLY 3.0 18.0 + - - +
39C VAL* 3.2 19.5 - - + +
41C SER* 1.3 70.6 - - - +
43C LEU* 1.3 62.2 + - + +
44C ALA 3.1 2.2 - - - -
45C MET* 3.0 11.3 + - + +
46C LEU* 2.9 25.2 + - - +
95C ASP* 3.2 36.6 - - + +
96C ALA 4.5 3.4 - - - +
97C ILE* 4.9 4.4 - - + +
165C LEU* 3.6 30.1 - - + +
166C VAL 3.6 17.0 - - - +
167C ASN* 4.1 7.9 - - + +
286C LEU* 5.3 1.3 - - + -
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 4.2 13.9 - - + -
39C VAL* 3.1 31.5 + - + +
40C ALA 4.1 1.1 - - - +
42C VAL* 1.3 81.2 - - + +
44C ALA* 1.3 65.5 + - - +
46C LEU* 3.1 23.2 + - + +
47C GLN* 3.1 26.0 + - - +
58C ILE* 4.0 23.4 - - + +
62C MET* 3.6 18.4 - - - -
165C LEU* 4.2 12.8 - - + -
286C LEU* 5.0 1.1 - - + -
290C LEU* 4.0 31.2 - - + -
295C MET* 4.2 9.6 - - - -
298C MET* 4.5 1.8 - - - -
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA 3.1 19.6 + - - +
41C SER* 3.4 9.6 - - - +
42C VAL 3.1 0.2 - - - -
43C LEU* 1.3 76.6 - - - +
45C MET* 1.3 60.4 + - - +
47C GLN* 3.3 24.1 - - - +
48C LEU 4.1 0.2 + - - -
62C MET* 3.9 13.8 - - + -
64C PHE* 4.8 5.4 - - + -
66C ILE* 3.9 12.4 - - + +
75C LEU* 4.3 24.2 - - + -
117C PHE* 3.6 12.3 - - + -
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Residues in contact with MET 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C SER* 3.3 16.4 + - - +
42C VAL* 3.0 12.2 + - - +
44C ALA* 1.3 78.3 - - - +
46C LEU* 1.3 63.8 + - - +
48C LEU* 3.2 19.8 + - - +
49C THR* 4.0 3.1 + - - +
95C ASP* 3.6 39.9 - - + +
96C ALA* 6.2 0.4 - - - -
97C ILE* 4.1 11.7 - - + -
113C PHE* 3.7 29.3 - - + -
117C PHE* 3.4 50.5 - - + +
119C SER* 5.3 7.2 - - - -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL 2.9 11.3 + - - +
43C LEU* 3.1 19.0 + - + +
45C MET* 1.3 74.6 - - - +
47C GLN* 1.3 59.9 + - - +
49C THR* 2.7 43.4 + - + +
50C THR* 3.0 10.3 + - - +
58C ILE* 4.3 8.3 - - + -
97C ILE* 4.3 19.5 - - + +
163C LEU* 5.3 2.9 - - + -
165C LEU* 3.7 23.6 - - + -
298C MET* 3.3 36.6 - - + -
306C PHE* 4.1 16.4 - - + -
317C VAL* 4.2 12.6 - - + -
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Residues in contact with GLN 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU 3.1 16.0 + - - +
44C ALA* 3.3 13.7 - - - +
45C MET 3.2 0.4 - - - -
46C LEU* 1.3 75.5 - - - +
48C LEU* 1.3 58.7 + - - +
50C THR* 3.3 15.3 - - + +
55C GLN* 3.0 28.2 + - - -
58C ILE* 3.9 17.7 - - + +
59C GLN* 3.5 22.8 + - + +
62C MET* 3.2 32.9 - - - +
64C PHE* 3.2 25.9 + - - +
65C LYS* 3.6 0.2 - - - -
66C ILE* 3.1 34.9 + - + +
67C ASP* 5.2 0.7 - - - +
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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