Contacts of the helix formed by residues 51 - 62 (chain B) in PDB entry 2E9V
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 ASN 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B VAL 3.6 5.3 + - - -
47B ASP* 2.8 19.0 - - - +
48B CYS* 2.5 43.5 + - - +
49B PRO 3.6 0.4 - - - -
50B GLU* 1.3 82.0 - - - +
52B ILE* 1.3 65.8 + - - +
53B LYS 3.3 0.6 - - - +
54B LYS* 3.4 12.6 + - - +
55B GLU* 3.4 11.3 + - - +
150B GLY* 4.4 11.3 - - - +
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Residues in contact with ILE 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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38B LYS* 4.8 1.8 - - + -
40B VAL* 3.6 23.1 - - + -
42B MET* 4.5 14.4 - - + -
48B CYS* 3.3 29.6 - - + +
51B ASN* 1.3 76.9 - - - +
53B LYS* 1.3 83.6 + - + +
55B GLU* 3.1 36.1 + - - +
56B ILE* 3.4 9.8 + - + +
80B GLN* 3.6 22.9 - - + -
82B LEU* 3.4 29.4 - - + -
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET* 4.7 16.6 - - - -
48B CYS 4.0 0.2 + - - -
49B PRO* 3.8 26.2 - - + +
50B GLU* 5.0 1.3 - - - -
51B ASN 3.3 0.8 - - - -
52B ILE* 1.3 88.4 - - + +
54B LYS* 1.3 61.0 - - - +
56B ILE* 3.2 14.6 + - + +
57B CYS* 3.1 21.5 + - - +
73B HIS* 4.2 14.6 - - - -
75B ARG* 4.6 8.1 - - - +
80B GLN* 3.5 25.4 + - - +
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Residues in contact with LYS 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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50B GLU* 4.2 14.8 - - - +
51B ASN* 3.4 10.9 + - - +
52B ILE 3.2 0.8 - - - -
53B LYS* 1.3 78.3 - - - +
55B GLU* 1.3 62.6 - - - +
57B CYS* 3.8 8.0 - - + +
58B ILE* 3.1 36.4 + - + +
129B ARG* 4.6 7.5 - - - +
149B PHE 5.1 0.4 - - - +
150B GLY 5.6 5.2 - - - +
151B LEU 6.1 0.2 - - - -
152B ALA 3.1 18.3 + - - +
153B THR* 2.9 37.6 + - - +
154B VAL* 5.1 1.1 - - - +
166B LYS* 5.8 1.0 - - - +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 2.7 35.6 + - - +
51B ASN 3.4 6.0 + - - +
52B ILE* 3.1 32.3 + - - +
54B LYS* 1.3 79.0 - - - +
56B ILE* 1.3 56.7 + - - +
58B ILE* 3.9 1.8 + - - +
59B ASN* 2.8 44.4 + - - +
82B LEU* 3.9 13.0 - - + +
84B LEU* 5.2 1.6 - - - +
148B ASP* 3.7 4.5 - - - +
149B PHE* 3.6 14.8 + - - +
150B GLY* 3.6 31.4 + - - +
2001B 85A 3.6 9.5 + - - -
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Residues in contact with ILE 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 ILE* 3.6 14.8 - - + +
53B LYS* 3.2 21.3 + - + +
54B LYS 3.1 0.4 - - - -
55B GLU* 1.3 74.3 - - - +
57B CYS* 1.3 65.8 + - - +
58B ILE 3.1 1.8 - - - -
59B ASN* 3.1 6.3 + - - +
60B LYS* 3.0 33.1 + - + +
70B PHE* 3.9 11.9 - - + -
73B HIS* 3.4 37.9 - - + +
80B GLN* 3.6 33.7 - - + +
82B LEU* 3.7 21.5 - - + -
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Residues in contact with CYS 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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65A GLU* 5.8 11.7 - - - -
53B LYS 3.1 13.8 + - - +
54B LYS* 3.4 9.8 + - + +
56B ILE* 1.3 78.5 - - - +
58B ILE* 1.3 64.0 + - + +
60B LYS* 3.8 22.1 + - - +
61B MET* 3.4 30.4 + - - +
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Residues in contact with ILE 58 (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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54B LYS* 3.1 29.5 + - + +
55B GLU 4.2 3.1 - - - +
56B ILE 3.1 0.2 - - - -
57B CYS* 1.3 79.8 - - + +
59B ASN* 1.3 65.6 + - - +
60B LYS 3.1 1.6 - - - -
61B MET* 3.0 25.9 + - - +
62B LEU* 3.2 14.9 - - + +
126B ILE* 4.0 28.7 - - + -
149B PHE* 4.3 21.1 - - + +
152B ALA* 3.1 38.8 - - + +
153B THR* 3.7 10.8 - - - +
154B VAL* 4.9 5.8 - - + +
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Residues in contact with ASN 59 (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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55B GLU* 2.8 42.4 + - - +
56B ILE* 3.1 7.0 + - - +
58B ILE* 1.3 77.3 - - - +
60B LYS* 1.3 61.0 + - - +
62B LEU* 3.4 34.3 + - - +
68B VAL* 4.3 6.6 - - - +
70B PHE* 3.6 49.2 - - + +
82B LEU* 5.0 3.4 - - - +
84B LEU* 3.6 16.7 - - - +
148B ASP* 6.0 0.4 - - - +
149B PHE* 4.2 17.6 - - - +
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Residues in contact with LYS 60 (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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65A GLU* 2.5 40.8 + - - +
66A ASN* 4.8 6.7 - - - +
109A ARG* 5.3 2.4 + - - -
113A GLN* 4.3 7.8 - - - +
116A ALA* 5.8 3.4 - - - +
143A ASN* 4.1 9.5 - - - +
56B ILE* 3.0 22.7 + - + +
57B CYS* 3.9 21.5 - - - +
58B ILE 3.1 0.6 - - - -
59B ASN* 1.3 76.5 - - - +
61B MET* 1.3 62.7 + - + +
62B LEU 3.4 4.2 + - - +
70B PHE* 3.8 24.5 - - + -
73B HIS* 6.0 1.8 - - + +
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Residues in contact with MET 61 (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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65A GLU* 6.6 0.4 - - + -
109A ARG* 4.7 1.0 + - - -
141A ARG* 3.2 59.3 - - - +
143A ASN* 3.4 24.9 + - - +
57B CYS* 3.4 31.0 - - - +
58B ILE* 3.0 13.3 + - + +
60B LYS* 1.3 77.4 - - + +
62B LEU* 1.3 62.6 - - - +
63B ASN* 5.0 0.2 - - - +
120B TYR* 3.8 8.1 + - - -
124B ILE* 4.4 1.2 - - - +
126B ILE* 4.2 6.7 - - + -
154B VAL* 4.0 20.9 - - + -
157B TYR* 6.5 1.1 - - + -
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Residues in contact with LEU 62 (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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109A ARG* 4.8 2.6 + - - -
58B ILE* 3.2 15.3 - - + +
59B ASN* 3.6 28.0 - - - +
60B LYS 3.2 4.8 - - - +
61B MET* 1.3 78.6 - - - +
63B ASN* 1.3 65.9 + - - +
67B VAL* 3.6 30.1 - - + -
68B VAL 4.9 2.7 - - - +
69B LYS* 6.1 0.5 - - - -
70B PHE* 5.7 3.6 + - + +
120B TYR* 3.9 4.0 - - + +
121B LEU* 4.1 15.0 - - + -
124B ILE* 4.2 2.7 - - + -
126B ILE* 3.3 33.7 - - + -
149B PHE* 3.6 30.5 - - + -
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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