Contacts of the helix formed by residues 44 - 63 (chain D) in PDB entry 2CVL
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 ASP 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D GLY* 1.3 75.4 - - - +
45D ILE* 1.3 68.2 + - + +
46D ARG* 3.0 12.3 + - - +
47D VAL* 2.9 32.1 + - - +
48D GLN* 3.0 21.8 + - - +
114D ARG* 3.6 13.2 - - - +
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Residues in contact with ILE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ASP* 1.3 80.0 - - + +
46D ARG* 1.3 60.5 + - + +
49D THR* 2.7 56.2 + - - +
77D LEU* 4.0 15.7 - - + -
82D ASP* 3.9 37.7 - - + +
85D GLY* 4.1 18.6 - - - -
86D PHE* 3.8 16.8 - - + +
114D ARG* 3.4 34.3 - - + +
115D VAL* 4.3 2.2 - - + -
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Residues in contact with ARG 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ASP* 3.0 12.8 + - - +
45D ILE* 1.3 85.9 - - + +
47D VAL* 1.3 60.5 + - + +
50D GLU* 2.9 52.5 + - - +
85D GLY* 4.9 3.6 - - - +
88D GLU* 4.5 17.2 + - - +
89D VAL* 3.5 24.7 - - + +
92D ARG* 3.4 24.8 - - - +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D VAL* 3.7 24.4 - - + +
42D GLU 4.0 10.3 - - - +
43D GLY* 4.5 3.1 - - - -
44D ASP* 2.9 35.2 + - - +
46D ARG* 1.3 79.3 - - + +
48D GLN* 1.3 62.4 + - - +
50D GLU* 3.5 16.4 + - - +
51D ARG* 3.2 20.6 + - - +
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Residues in contact with GLN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PRO* 3.3 25.5 - - + +
40D LEU* 6.1 1.4 - - - +
41D VAL* 3.8 22.7 - - - +
42D GLU* 4.9 0.9 - - - -
43D GLY 3.1 20.2 + - - +
44D ASP 3.0 19.1 + - - +
45D ILE 4.1 1.6 - - - +
47D VAL* 1.3 73.5 - - + +
49D THR* 1.3 66.5 + - - +
51D ARG* 3.2 5.0 + - - +
52D VAL* 3.1 24.4 + - - +
113D VAL* 4.1 3.3 - - - +
114D ARG* 3.1 52.3 + - + +
115D VAL* 3.9 9.8 - - + +
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Residues in contact with THR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ILE* 2.7 43.5 + - - +
46D ARG 3.8 2.7 - - - -
48D GLN* 1.3 76.5 - - - +
50D GLU* 1.3 58.0 + - - +
52D VAL* 3.1 4.7 + - + +
53D MSE 2.8 37.8 + - + +
86D PHE* 3.6 38.3 - - + +
89D VAL* 3.6 27.1 - - + -
90D TYR 4.3 1.6 - - - +
115D VAL* 4.0 8.3 - - + +
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ARG* 2.9 41.0 + - - +
47D VAL* 3.6 21.3 + - - +
48D GLN 3.2 0.2 - - - -
49D THR* 1.3 77.8 - - - +
51D ARG* 1.3 56.4 + - - +
53D MSE 3.3 3.1 + - - +
54D GLU* 2.9 34.9 + - + +
89D VAL* 3.5 21.8 - - + -
92D ARG* 3.0 33.5 + - - +
93D TYR* 3.9 10.5 + - - +
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ARG 4.4 4.9 + - - -
33D PRO* 3.6 24.5 - - + -
34D LEU 3.6 9.5 + - - +
35D ALA* 4.1 3.2 - - - +
36D PRO* 3.7 29.8 - - - +
41D VAL* 3.5 35.2 - - + -
47D VAL 3.2 9.8 + - - +
48D GLN 3.2 9.8 + - - +
50D GLU* 1.3 78.3 - - - +
52D VAL* 1.3 63.4 + - - +
54D GLU* 3.4 26.1 + - - +
55D ASN* 2.8 44.7 + - - +
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLN* 3.6 23.3 - - + +
32D ILE 3.5 5.2 - - - -
33D PRO* 3.5 28.7 - - + -
48D GLN 3.1 14.0 + - - +
49D THR* 3.5 9.2 - - - +
51D ARG* 1.3 77.3 - - - +
53D MSE 1.3 63.3 + - + +
55D ASN* 3.2 10.1 + - - +
56D LEU* 2.9 28.1 + - + +
115D VAL* 3.8 14.4 - - + +
117D VAL* 3.8 31.4 - - + -
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Residues in contact with MSE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D THR* 2.8 28.4 + - + +
50D GLU 3.6 3.1 - - - +
52D VAL* 1.3 87.8 - - + +
54D GLU* 1.3 57.4 + - - +
56D LEU* 3.2 33.0 + - + +
57D LYS* 2.9 29.8 + - - +
67D LEU* 4.7 2.5 - - - +
89D VAL* 4.1 8.5 - - + +
90D TYR* 4.1 25.1 - - + -
93D TYR* 3.5 48.3 - - + -
94D PHE* 3.8 23.3 - - + -
117D VAL* 4.0 13.7 - - + -
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Residues in contact with GLU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLU* 2.9 22.8 + - + +
51D ARG* 3.5 26.5 + - - +
53D MSE 1.3 75.7 - - - +
55D ASN* 1.3 59.6 + - - +
57D LYS* 3.4 20.5 + - - +
58D ALA* 2.9 29.3 + - - +
93D TYR* 2.6 32.8 + - - +
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Residues in contact with ASN 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA* 4.2 6.8 - - + -
10D PRO* 3.3 25.4 - - + +
31D GLN* 3.5 21.7 - - + +
32D ILE 3.0 27.5 + - - -
34D LEU 3.0 15.8 + - - +
51D ARG* 2.8 41.3 + - - +
52D VAL* 3.2 7.4 + - - +
54D GLU* 1.3 74.9 - - - +
56D LEU* 1.3 65.4 + - - +
58D ALA* 3.3 1.7 + - - +
59D VAL* 3.0 30.3 + - - +
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 3.9 16.2 - - + -
31D GLN* 3.6 22.4 - - + +
52D VAL 2.9 14.2 + - - +
53D MSE 3.2 42.1 + - + +
55D ASN* 1.3 77.5 - - - +
57D LYS* 1.3 57.1 + - - +
59D VAL* 3.3 3.4 + - - +
60D LEU* 2.8 42.3 + - + +
67D LEU* 4.6 4.0 - - + -
94D PHE* 4.8 11.7 - - + -
117D VAL* 3.6 32.1 - - + +
118D ALA 4.8 0.2 - - - -
119D CYS* 4.0 18.4 - - + -
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Residues in contact with LYS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ARG* 5.5 1.6 - - - +
53D MSE 2.9 17.2 + - - +
54D GLU* 3.6 26.0 + - - +
56D LEU* 1.3 77.3 - - - +
58D ALA* 1.3 57.9 + - - +
60D LEU* 3.7 2.5 - - - +
61D GLU* 2.9 65.8 + - + +
67D LEU* 3.9 36.5 - - + +
93D TYR* 4.9 3.9 - - + -
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D THR* 4.1 1.7 - - - +
8D ARG* 2.9 74.0 + - + +
9D ALA* 4.1 2.7 - - + -
54D GLU 2.9 17.2 + - - +
55D ASN 3.7 4.0 - - - +
57D LYS* 1.3 77.2 - - - +
59D VAL* 1.3 62.1 + - - +
62D ALA* 3.1 12.6 + - - +
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Residues in contact with VAL 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.9 4.9 - - + +
6D THR* 4.3 9.0 - - + -
9D ALA* 3.6 21.1 - - + -
18D GLN* 3.9 26.9 - - + +
19D ALA* 3.3 32.3 - - + -
28D VAL* 4.0 13.0 - - + -
31D GLN* 4.2 13.9 - - - +
55D ASN 3.0 19.7 + - - +
56D LEU 3.8 2.9 - - - +
58D ALA* 1.3 72.6 - - - +
60D LEU* 1.3 66.8 + - - +
62D ALA* 3.3 3.3 + - - +
63D ALA* 3.1 20.8 + - - +
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D VAL* 4.5 3.6 - - + -
28D VAL* 3.7 23.6 - - + -
56D LEU* 2.8 22.5 + - + +
57D LYS 3.7 3.8 - - - +
59D VAL* 1.3 76.7 - - - +
61D GLU* 1.3 60.6 + - - +
63D ALA* 3.1 11.9 + - - +
65D SER* 2.8 35.1 + - - +
66D GLY* 3.9 15.7 - - - +
67D LEU* 3.8 21.1 - - + -
70D VAL* 3.5 25.1 - - + -
119D CYS* 4.2 8.1 - - - -
121D ALA* 3.6 30.5 - - + -
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ARG* 3.0 28.8 + - - +
57D LYS* 2.9 55.1 + - + +
60D LEU* 1.3 71.9 - - - +
62D ALA* 1.3 57.7 + - - +
63D ALA 3.0 4.9 - - - -
64D GLY* 3.0 17.7 + - - -
65D SER 3.5 15.0 - - - +
66D GLY* 4.6 8.6 - - - -
67D LEU 5.8 0.2 + - - -
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.9 12.7 - - + +
5D LYS 4.9 2.5 - - - +
6D THR* 3.6 30.7 - - + +
8D ARG* 3.9 6.0 - - - +
58D ALA 3.1 18.1 + - - +
59D VAL 3.7 4.9 - - - +
60D LEU 3.3 0.4 - - - -
61D GLU* 1.3 76.3 - - - +
63D ALA* 1.3 57.9 + - - +
64D GLY 3.2 1.2 + - - -
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.6 26.5 - - + -
19D ALA* 5.1 0.2 - - + -
21D LYS* 3.2 33.4 + - + +
26D VAL* 3.7 29.2 - - + +
59D VAL 3.1 10.8 + - - +
60D LEU 3.1 10.5 + - - +
61D GLU 3.0 0.8 - - - -
62D ALA* 1.3 79.7 - - - +
64D GLY* 1.3 58.9 + - - +
65D SER 3.2 0.6 + - - -
123D ALA* 5.8 0.2 - - - -
124D GLU 5.5 1.9 + - - -
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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