Contacts of the helix formed by residues 47 - 57 (chain B) 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 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.0 20.2 - - + -
19B ALA* 3.7 27.1 - - + -
36B PRO* 2.8 26.4 + - + +
45B ARG* 4.8 1.8 - - + -
46B ILE* 1.3 73.7 - - - +
48B ASP* 1.3 70.8 + - - +
49B PHE 3.1 1.0 + - - -
50B ALA* 3.4 4.1 + - - +
51B LEU* 3.2 38.6 + - + +
64B VAL* 4.0 14.4 - - + -
73B LEU* 4.0 22.0 - - + -
76B HIS* 4.3 10.3 - - + +
77B LEU* 4.4 2.5 - - + -
134B GLY* 3.5 16.4 - - - +
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 4.2 0.9 - - + -
45B ARG 2.8 28.5 + - - +
46B ILE 3.0 0.6 + - - -
47B ILE* 1.3 78.4 - - - +
49B PHE* 1.3 57.5 + - - +
51B LEU* 3.8 5.8 - - - +
52B SER* 2.7 35.6 + - - -
76B HIS* 2.7 28.0 + - - -
81B TRP* 3.0 15.4 + - - -
299B ILE* 4.1 10.1 - - + -
300B TRP 3.4 16.2 - - - +
301B THR* 2.6 27.5 + - - -
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 3.9 24.9 - + + -
41B GLY* 6.2 0.2 - - - -
44B ALA* 4.5 12.3 - - + -
45B ARG 4.0 11.2 - - - -
46B ILE* 3.7 15.3 - - - +
47B ILE 3.1 0.8 - - - -
48B ASP* 1.3 77.8 - - - +
50B ALA* 1.3 52.7 + - - +
52B SER* 3.1 2.6 + - - -
53B ASN* 2.7 40.9 + - - +
136B HIS 4.1 10.3 - - - +
137B ILE* 3.6 33.0 - - + -
138B TYR* 3.7 23.3 - - - +
139B LYS* 4.6 5.8 - - + -
290B LEU* 4.7 15.0 - - + -
292B ILE* 6.4 0.4 - - + -
299B ILE* 3.6 38.9 - - + +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.9 7.2 - - + -
46B ILE 4.5 1.0 + - - +
47B ILE 3.4 7.8 + - - +
49B PHE* 1.3 77.7 - - - +
51B LEU* 1.3 62.6 + - - +
53B ASN* 3.2 14.1 + - - +
54B ALA* 3.1 22.5 + - - +
132B LEU* 4.4 13.6 - - + +
133B ALA 4.0 20.4 - - - +
134B GLY* 4.6 9.2 - - - -
136B HIS 4.9 2.8 + - - +
138B TYR* 4.4 13.2 - - + +
142B TYR* 3.9 6.3 + - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.0 11.9 - - + -
47B ILE* 3.2 31.1 + - + +
48B ASP 3.8 0.2 - - - +
50B ALA* 1.3 77.1 - - - +
52B SER* 1.3 62.2 + - - +
54B ALA* 3.2 8.5 + - - +
55B LEU* 3.1 21.1 + - - +
62B ILE* 3.8 17.8 - - + +
64B VAL* 3.9 11.2 - - + -
77B LEU* 3.7 22.9 - - + -
81B TRP* 3.4 45.8 - - + +
92B PHE* 3.7 24.7 - - + -
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASP 2.7 27.1 + - - -
49B PHE 3.7 2.2 - - - -
51B LEU* 1.3 70.3 - - - +
53B ASN* 1.3 66.4 + - - +
55B LEU* 4.2 4.3 - - - -
56B ASN* 2.9 32.4 + - - +
81B TRP* 3.7 9.3 - - - -
298B PRO 3.7 19.3 - - - -
299B ILE* 3.6 12.8 - - - -
300B TRP* 2.9 30.0 + - - -
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE 2.7 23.4 + - - +
50B ALA* 3.4 2.4 - - - +
52B SER* 1.3 73.2 - - - +
54B ALA* 1.3 56.3 + - - +
57B SER* 2.9 34.1 + - - -
138B TYR* 3.0 39.0 + - - +
139B LYS* 3.2 5.7 - - - +
140B MET 2.9 27.1 + - - +
142B TYR* 3.2 32.9 + - + +
297B TRP* 3.0 19.8 + - - +
299B ILE* 5.5 0.9 - - - +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA* 3.8 29.2 - - + -
17B VAL* 6.3 0.7 - - + -
50B ALA 3.1 11.8 + - - +
51B LEU* 3.2 8.3 + - - +
53B ASN* 1.3 76.5 - - - +
55B LEU* 1.3 60.8 + - - +
57B SER* 3.4 1.8 + - - -
58B GLY 3.4 3.5 + - - -
59B ILE* 3.0 36.8 + - + +
62B ILE* 4.1 12.8 - - + -
132B LEU* 4.7 0.9 - - + -
142B TYR* 3.4 15.8 - - + -
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU 3.1 13.0 + - - +
52B SER* 3.6 7.2 - - - +
54B ALA* 1.3 77.4 - - - +
56B ASN* 1.3 72.6 + - - +
58B GLY* 3.1 15.1 + - - -
59B ILE 4.2 8.1 - - - +
62B ILE* 4.9 2.2 - - + +
81B TRP* 3.9 25.6 - - + -
83B PHE* 4.0 28.3 - - + -
84B PHE* 4.3 15.5 - - + -
300B TRP* 4.4 13.2 - - + -
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Residues in contact with ASN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B SER 2.9 20.5 + - - +
55B LEU* 1.3 83.3 - - - +
57B SER* 1.3 60.0 + - - +
58B GLY 3.4 0.5 + - - -
297B TRP* 3.3 65.2 - - + -
298B PRO* 3.0 40.4 + - - +
11D ARG* 4.1 11.3 + - - -
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA* 3.2 16.7 - - - +
53B ASN 2.9 21.9 + - - -
54B ALA* 3.7 5.8 - - - -
55B LEU 3.2 0.6 - - - -
56B ASN* 1.3 78.2 - - - +
58B GLY* 1.3 56.8 + - - +
59B ILE* 3.4 5.2 - - - -
141B ASP* 3.4 11.4 - - - -
142B TYR* 2.8 43.8 + - - -
143B GLU* 4.3 2.8 - - - +
297B TRP* 3.7 1.9 - - - -
11D ARG* 3.3 23.4 + - - +
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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