Contacts of the helix formed by residues 35 - 50 (chain A) in PDB entry 3CVM
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PHE* 1.3 77.6 - - - +
36A PRO* 1.3 65.6 - - - +
38A GLY 3.2 14.4 + - - -
39A VAL* 3.2 11.8 + - - +
169A LEU* 3.4 6.6 - - - +
322A GLN* 2.8 29.3 + - - -
337A SER* 3.1 35.4 + - - -
371A LEU 2.7 19.9 + - - -
372A PHE* 4.2 2.9 - - - -
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Residues in contact with PRO 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA 4.2 1.7 - - - +
13A SER* 4.4 4.7 - - - +
16A GLY* 3.7 29.2 - - - +
17A VAL* 3.9 4.0 - - + +
34A PHE* 3.4 20.9 - - + +
35A SER* 1.3 84.2 - - - +
37A TYR* 1.3 57.8 + - - +
39A VAL* 3.2 5.2 - - + +
40A ALA* 3.1 27.7 + - - +
370A VAL* 3.4 37.5 - - + +
371A LEU 3.9 6.7 - - - +
372A PHE* 4.1 0.9 - - - -
373A MET* 3.6 22.2 - - + -
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Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 5.1 13.0 - - + -
13A SER* 6.2 0.4 - - - +
35A SER* 3.3 1.9 + - - +
36A PRO* 1.3 77.1 - - - +
38A GLY* 1.3 65.2 + - - +
40A ALA* 4.3 4.3 - - + -
41A SER* 2.8 47.3 + - - -
75A LEU* 4.9 2.9 + - + -
78A LEU* 3.6 24.7 - - + +
79A TYR* 3.4 33.3 + - - +
82A LEU* 3.7 15.5 - - + +
93A THR* 3.6 26.1 + - - +
167A ASN* 5.0 0.7 - - - -
169A LEU* 4.2 12.8 - - + -
369A THR* 3.8 20.9 - - + -
370A VAL 3.2 15.2 + - - +
371A LEU* 4.2 17.0 - - + -
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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
----------------------------------------------------------
35A SER* 3.2 22.2 + - - -
37A TYR* 1.3 79.9 - - - +
39A VAL* 1.3 60.7 + - - +
41A SER* 3.6 2.8 - - - -
42A VAL* 3.4 22.5 + - - +
167A ASN* 3.8 18.5 - - - +
169A LEU* 5.2 0.9 - - - -
337A SER* 4.8 2.0 - - - -
339A THR* 3.4 19.7 + - - -
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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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15A PHE* 4.4 3.8 - - + -
16A GLY* 3.9 17.9 - - - -
19A VAL* 4.4 10.8 - - + -
34A PHE* 3.9 15.5 - - + -
35A SER 3.2 12.5 + - - +
36A PRO 3.2 13.7 - - - +
38A GLY* 1.3 71.8 - - - +
40A ALA* 1.3 70.1 + - - +
42A VAL* 3.1 6.3 - - + +
43A LEU* 3.1 51.0 + - + +
286A LEU* 4.0 27.4 - - + -
290A LEU* 4.7 1.8 - - + -
322A GLN* 3.8 4.7 - - - +
339A THR* 3.7 5.6 + - + -
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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
----------------------------------------------------------
12A ALA* 3.6 39.0 - - + +
15A PHE* 4.1 17.3 - - + -
36A PRO 3.1 15.1 + - - +
37A TYR* 3.9 5.4 - - + +
38A GLY 3.4 0.2 - - - -
39A VAL* 1.3 82.4 - - - +
41A SER* 1.3 63.1 + - - +
44A ALA* 3.1 22.2 + - - +
62A MET* 3.6 10.0 - - + +
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Residues in contact with SER 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 TYR* 2.8 46.1 + - - -
38A GLY 3.6 5.6 - - - -
39A VAL 3.2 0.2 - - - -
40A ALA* 1.3 76.0 - - - +
42A VAL* 1.3 62.9 + - - +
44A ALA* 3.0 22.5 + - - +
45A MET* 3.3 10.9 + - - +
95A ASP* 4.2 11.6 - - - +
117A PHE* 4.9 1.2 - - - -
167A ASN* 3.8 19.6 + - - -
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY 3.4 6.7 + - - +
39A VAL* 3.1 13.5 - - + +
41A SER* 1.3 75.0 - - - +
43A LEU* 1.3 88.1 + - + +
45A MET* 3.1 16.7 + - + +
46A LEU* 3.0 19.9 + - - +
165A LEU* 4.5 8.2 - - + +
166A VAL* 4.1 6.1 - - - -
167A ASN* 3.5 26.7 - - + +
286A LEU* 5.7 0.2 - - + -
339A THR* 3.4 43.1 - - + +
341A VAL* 4.6 13.1 - - + +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.2 35.0 - - + -
39A VAL* 3.1 19.8 + - + +
40A ALA 4.3 0.9 - - - +
42A VAL* 1.3 89.0 - - + +
44A ALA* 1.3 60.9 + - - +
46A LEU* 3.3 17.6 + - + +
47A GLN* 3.1 24.3 + - - +
58A ILE* 4.0 7.4 - - + +
62A MET* 3.8 16.2 - - - -
286A LEU* 5.9 1.1 - - + -
290A LEU* 3.5 31.6 - - + -
295A MET* 4.3 8.7 - - - -
298A MET* 5.5 1.6 - - + -
341A VAL* 4.1 18.2 - - + -
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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 3.1 14.0 + - - +
41A SER* 3.0 17.1 + - - +
43A LEU* 1.3 77.9 - - - +
45A MET* 1.3 59.9 + - - +
47A GLN* 3.3 23.3 - - - +
48A LEU 4.0 1.2 + - - -
62A MET* 4.2 11.8 - - + -
64A PHE* 5.2 3.6 - - + -
66A ILE* 4.3 7.7 - - + +
75A LEU* 4.3 16.6 - - + -
117A PHE* 3.7 23.7 - - + -
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Residues in contact with MET 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 SER 3.3 6.3 + - - +
42A VAL* 3.1 18.3 + - - +
44A ALA* 1.3 76.8 - - - +
46A LEU* 1.3 62.8 + - - +
48A LEU* 3.0 21.5 + - - +
49A THR* 3.8 8.0 + - - +
95A ASP* 3.9 27.6 - - + +
96A ALA 4.0 3.1 - - - +
97A ILE* 4.2 4.3 - - - -
113A PHE* 3.7 30.3 - - + -
117A PHE* 3.7 30.7 - - + -
119A SER* 4.6 1.1 - - - -
165A LEU* 3.8 20.6 - - + +
166A VAL 3.7 39.3 - - - +
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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 VAL 3.0 12.1 + - - +
43A LEU* 3.4 27.1 - - + +
44A ALA 3.2 0.2 - - - -
45A MET* 1.3 74.4 - - - +
47A GLN* 1.3 64.3 + - - +
49A THR* 2.7 33.9 + - - +
50A THR* 3.3 12.1 + - + +
58A ILE* 3.9 14.8 - - + -
165A LEU* 3.9 15.6 - - + +
298A MET* 3.8 29.6 - - + -
306A PHE* 3.8 16.6 - - + -
317A VAL* 4.7 2.5 - - + -
341A VAL* 3.8 31.0 - - + -
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Residues in contact with GLN 47 (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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43A LEU 3.1 11.0 + - - +
44A ALA* 3.3 13.0 - - - +
46A LEU* 1.3 76.1 - - - +
48A LEU* 1.3 59.7 + - - +
50A THR* 3.4 11.8 + - - -
55A GLN* 3.1 27.4 + - - +
58A ILE* 3.6 22.3 - - + +
59A GLN* 3.1 33.8 + - + +
62A MET* 3.7 22.2 - - - +
64A PHE* 3.0 29.3 + - - -
66A ILE* 2.9 36.3 + - + +
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Residues in contact with LEU 48 (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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45A MET 3.0 10.2 + - - +
46A LEU 3.0 0.2 + - - -
47A GLN* 1.3 79.9 - - - +
49A THR* 1.3 59.2 + - + +
50A THR 3.3 0.4 - - - -
55A GLN* 5.0 1.6 + - - +
66A ILE* 3.7 22.7 - - + -
67A ASP* 4.6 4.0 - - + +
109A PHE* 4.1 17.1 - - + -
112A HIS* 4.0 26.5 - - + +
113A PHE* 3.9 30.3 - - + +
116A LEU* 4.0 10.8 - - + -
117A PHE* 3.5 37.5 - - + -
308A SER* 3.2 21.0 - - - -
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Residues in contact with THR 49 (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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45A MET 4.0 11.2 - - - +
46A LEU* 2.7 24.1 + - - +
48A LEU* 1.3 78.5 - - - +
50A THR* 1.3 59.5 + - - +
109A PHE* 4.0 21.8 - - + -
113A PHE* 5.9 1.8 - - + -
163A LEU* 4.0 21.3 - - + -
165A LEU* 4.2 9.6 - - + -
306A PHE* 3.3 39.8 - - - -
308A SER* 3.8 2.9 - - - -
309A LEU* 3.2 30.7 + - + +
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Residues in contact with THR 50 (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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46A LEU* 3.3 20.5 + - + +
47A GLN* 3.4 10.0 + - - -
49A THR* 1.3 88.9 - - - +
51A GLY* 1.3 58.7 + - - +
54A THR* 3.6 27.6 - - + -
55A GLN* 3.1 34.2 + - - +
58A ILE* 3.9 9.9 - - + +
305A ASP 3.2 10.1 - - - +
306A PHE* 3.8 17.3 - - + -
308A SER* 2.8 19.3 + - - -
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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
------------------------------------------------------------
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