Contacts of the helix formed by residues 46 - 57 (chain A) in PDB entry 6V99
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 ILE 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 5.6 0.9 - - + -
35A LYS* 3.5 25.4 - - + +
36A PRO* 3.6 6.9 + - + +
38A VAL* 2.9 35.0 + - + +
39A TYR 5.0 0.4 - - - +
40A PHE* 4.2 15.9 - - + -
45A ARG* 1.3 72.8 - - - +
47A ILE* 1.3 65.3 + - - +
48A ASP 3.1 0.5 + - - -
49A PHE* 3.2 25.2 + - - +
50A ALA* 4.4 0.9 + - - +
134A GLY 4.0 1.6 - - - +
135A ASP* 3.5 37.9 - - - +
136A HIS 3.8 11.4 - - - +
137A ILE* 4.2 7.6 - - + -
270A VAL* 3.8 24.5 - - + -
276A TYR* 5.0 1.8 - - + -
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Residues in contact with ILE 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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17A VAL* 4.3 11.9 - - + -
19A ALA* 3.8 22.9 - - + -
36A PRO* 3.0 20.9 + - + +
45A ARG* 4.7 2.2 - - + -
46A ILE* 1.3 77.5 - - - +
48A ASP* 1.3 75.9 + - - +
49A PHE 3.0 2.1 + - - -
50A ALA* 3.2 4.4 + - - +
51A LEU* 3.2 33.9 + - + +
64A VAL* 3.9 16.6 - - + -
73A LEU* 3.8 27.6 - - + -
76A HIS* 4.2 12.3 - - + +
77A LEU* 4.2 8.3 - - + -
134A GLY* 3.6 19.1 - - - +
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Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 4.1 1.3 - - + -
45A ARG 2.8 29.4 + - - +
47A ILE* 1.3 78.2 - - - +
49A PHE* 1.3 55.7 + - - +
51A LEU* 4.0 5.3 - - - +
52A SER* 2.7 37.0 + - - -
76A HIS* 2.7 26.8 + - - -
81A TRP* 3.1 15.1 + - - -
299A ILE* 4.0 11.2 - - + -
300A TRP 3.4 15.5 - - - +
301A THR* 2.3 30.7 + - - -
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Residues in contact with PHE 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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40A PHE* 4.0 25.8 - + + -
44A ALA* 4.5 8.7 - - + -
45A ARG 3.7 14.8 - - - -
46A ILE 3.5 16.4 - - - +
47A ILE 3.0 1.4 + - - -
48A ASP* 1.3 75.4 - - - +
50A ALA* 1.3 61.8 + - - +
52A SER* 3.2 5.2 + - - -
53A ASN* 2.8 36.8 + - - +
136A HIS 3.9 10.1 - - - +
137A ILE* 3.8 31.9 - - + -
138A TYR* 3.7 22.2 - - + +
139A LYS* 4.7 5.4 - - + -
290A LEU* 4.6 12.1 - - + -
292A ILE* 6.5 0.2 - - + -
299A ILE* 3.6 39.2 - - + +
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Residues in contact with ALA 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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17A VAL* 4.6 11.0 - - + -
46A ILE 4.4 0.8 + - - -
47A ILE* 3.2 8.5 + - - +
49A PHE* 1.3 77.6 - - - +
51A LEU* 1.3 63.2 + - - +
53A ASN* 3.4 11.4 + - - +
54A ALA* 3.1 22.7 + - - +
132A LEU* 4.2 11.9 - - + +
133A ALA 4.0 20.2 - - - +
134A GLY* 4.3 11.2 - - - -
136A HIS 4.8 2.9 + - - +
138A TYR* 4.5 10.7 - - + +
142A TYR* 4.0 5.8 + - - +
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Residues in contact with LEU 51 (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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17A VAL* 3.8 17.9 - - + -
47A ILE* 3.2 30.3 + - + +
50A ALA* 1.3 77.9 - - - +
52A SER* 1.3 55.7 + - - +
54A ALA* 3.2 6.7 + - - +
55A LEU* 3.0 28.6 + - - +
62A ILE* 3.7 32.0 - - + +
64A VAL* 3.9 11.4 - - + -
77A LEU* 3.7 23.6 - - + -
81A TRP* 3.4 47.6 - - + +
92A PHE* 3.9 6.1 - - + -
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Residues in contact with SER 52 (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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48A ASP 2.7 24.6 + - - -
49A PHE 3.7 2.7 - - - -
51A LEU* 1.3 73.0 - - - +
53A ASN* 1.3 57.4 + - - +
55A LEU* 4.2 4.7 - - - -
56A ASN* 2.7 42.5 + - - -
81A TRP* 3.8 7.8 - - - -
298A PRO 3.7 18.2 - - - -
299A ILE* 3.4 12.8 - - - -
300A TRP* 2.8 29.6 + - - -
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Residues in contact with ASN 53 (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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49A PHE 2.8 23.3 + - - +
50A ALA 3.5 0.9 - - - +
52A SER* 1.3 73.5 - - - +
54A ALA* 1.3 55.7 + - - +
57A SER* 2.7 36.9 + - - -
138A TYR* 3.0 49.2 + - - +
139A LYS* 3.3 6.6 - - - +
140A MET 3.1 17.1 + - - +
142A TYR* 3.3 22.0 + - + +
297A TRP* 2.8 27.7 + - - +
299A ILE* 5.5 0.9 - - - +
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Residues in contact with ALA 54 (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 ALA* 3.8 29.6 - - + -
17A VAL* 6.1 0.4 - - + -
50A ALA 3.1 13.6 + - - +
51A LEU* 3.6 7.4 - - - +
53A ASN* 1.3 76.0 - - - +
55A LEU* 1.3 64.5 + - - +
57A SER* 3.2 2.8 + - - -
58A GLY 3.2 4.3 + - - -
59A ILE* 3.0 33.3 + - + +
62A ILE* 4.2 11.9 - - + -
132A LEU* 4.6 1.3 - - + -
142A TYR* 3.5 15.2 - - + -
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Residues in contact with LEU 55 (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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51A LEU 3.0 16.2 + - - +
52A SER* 3.6 4.7 - - - +
54A ALA* 1.3 75.9 - - - +
56A ASN* 1.3 68.7 + - - +
58A GLY* 2.9 21.5 + - - -
59A ILE 4.2 8.8 + - - +
62A ILE* 4.7 3.2 - - + +
81A TRP* 4.1 20.2 - - + -
83A PHE* 3.9 23.8 - - + -
84A PHE* 4.0 16.8 - - + -
298A PRO 5.8 0.7 - - - +
300A TRP* 4.5 6.5 - - + -
60C ARG* 4.9 3.3 + - - -
88C ARG* 3.9 28.7 - - + +
90C GLU* 5.7 3.1 - - - +
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Residues in contact with ASN 56 (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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52A SER* 2.7 24.7 + - - +
55A LEU* 1.3 86.3 - - - +
57A SER* 1.3 59.9 + - - +
58A GLY 3.2 0.9 + - - -
297A TRP* 3.3 60.8 - - + -
298A PRO* 3.0 41.2 + - - +
11C ARG* 4.1 6.8 - - - -
60C ARG* 3.8 25.0 + - - +
88C ARG* 5.4 4.0 - - - +
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Residues in contact with SER 57 (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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10A ALA* 3.2 18.6 - - - +
53A ASN 2.7 24.4 + - - -
54A ALA 3.7 4.3 - - - -
55A LEU 3.2 0.4 - - - -
56A ASN* 1.3 75.5 - - - +
58A GLY* 1.3 57.7 + - - +
59A ILE* 4.6 3.8 - - - -
140A MET 3.5 1.6 + - - -
141A ASP* 3.5 12.3 - - - -
142A TYR* 2.9 42.9 + - - -
143A GLU* 4.4 2.7 - - - +
297A TRP* 3.5 1.9 - - - -
8C PRO* 5.9 0.5 - - - +
11C ARG* 3.5 22.3 + - - +
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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
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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