Contacts of the helix formed by residues 45 - 58 (chain E) in PDB entry 6R93
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 GLY 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44E PRO* 1.3 72.3 - - - +
46E THR* 1.3 61.5 + - - +
48E ALA* 3.4 4.9 + - - +
49E LEU* 3.0 32.7 + - - +
45F LYS* 3.7 23.3 - - - -
81I A 3.4 4.4 + - - -
82I A 2.6 22.9 + - - -
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Residues in contact with THR 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E TYR* 4.3 17.5 - - + -
43E ARG* 3.5 12.2 + - - +
44E PRO 3.7 0.6 + - - -
45E GLY* 1.3 75.7 - - - +
47E VAL* 1.3 57.9 + - - +
49E LEU* 3.2 15.4 + - + +
50E ARG* 3.0 39.4 + - + +
53E ARG* 5.1 0.3 + - - -
82I A 3.5 0.2 + - - -
142J T 4.2 24.9 - - - +
143J G 3.7 23.3 + - - -
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Residues in contact with VAL 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TYR* 5.5 6.9 - - + +
43E ARG 4.9 0.8 + - - -
46E THR* 1.3 77.3 - - - +
48E ALA* 1.3 60.4 + - - +
50E ARG* 2.9 24.5 + - + +
51E GLU* 2.8 41.5 + - + +
82I A 2.9 58.3 + - - +
83I C 4.4 11.4 - - - +
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Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLY* 3.6 9.2 - - - +
46E THR 3.3 0.2 - - - -
47E VAL* 1.3 78.5 - - - +
49E LEU* 1.3 58.0 + - - +
51E GLU* 3.1 7.2 + - - +
52E ILE* 2.9 32.2 + - - +
40F ARG* 3.3 39.9 - - - +
45F LYS* 3.9 16.4 - - + +
81I A 4.7 0.9 - - - +
82I A 3.0 18.6 + - - +
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Residues in contact with LEU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ILE* 4.7 10.5 - - + -
116C LEU* 4.8 4.9 - - + +
117C LEU* 4.4 21.8 - - + +
118C PRO* 4.1 28.7 - - + -
45E GLY 3.0 24.6 + - - +
46E THR* 3.3 11.9 - - + +
47E VAL 3.1 0.2 - - - -
48E ALA* 1.3 77.5 - - - +
50E ARG* 1.3 61.0 + - - +
52E ILE* 3.1 21.8 + - + +
53E ARG* 3.0 47.8 + - - +
45F LYS* 4.6 18.2 - - + +
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Residues in contact with ARG 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TYR* 2.9 44.8 + - - -
46E THR* 3.0 22.9 + - + +
47E VAL* 2.9 30.0 + - + +
49E LEU* 1.3 75.7 - - - +
51E GLU* 1.3 58.4 + - + +
53E ARG* 3.4 14.5 + - - +
54E ARG* 2.9 30.9 + - - +
7I A 3.4 40.7 + - - -
8I T 4.3 18.5 + - - +
141J T 5.3 2.8 + - - -
142J T 3.8 22.4 + - - +
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Residues in contact with GLU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 2.8 30.2 + - + +
48E ALA* 3.1 10.3 + - - +
50E ARG* 1.3 75.5 - - - +
52E ILE* 1.3 66.1 + - - +
54E ARG* 3.8 29.3 + - - +
55E TYR* 2.9 47.6 + - + +
36F ARG* 5.6 7.8 - - - +
37F ARG* 5.3 3.6 - - - +
40F ARG* 3.8 26.3 + - - -
82I A 4.5 4.3 + - - -
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Residues in contact with ILE 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ILE* 3.7 31.4 - - + -
116C LEU* 5.1 0.9 - - + -
48E ALA 2.9 22.4 + - - +
49E LEU* 3.1 27.8 + - + +
51E GLU* 1.3 75.8 - - - +
53E ARG* 1.3 59.5 + - + +
55E TYR* 4.4 0.2 - - - +
56E GLN* 2.9 49.3 + - - +
40F ARG* 3.5 33.2 - - - +
43F GLY* 4.2 16.6 - - - +
44F VAL 4.1 15.3 - - - +
45F LYS* 4.7 7.2 - - + -
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Residues in contact with ARG 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ILE* 4.9 18.5 - - + +
117C LEU* 5.3 4.4 - - - +
118C PRO* 4.7 17.6 - - - +
46E THR 5.1 0.4 + - - -
49E LEU* 3.0 48.0 + - - +
50E ARG* 3.9 13.4 - - - +
52E ILE* 1.3 77.1 - - + +
54E ARG* 1.3 62.8 + - - +
56E GLN* 3.8 5.3 - - - +
57E LYS* 3.0 26.9 + - - +
142J T 5.8 1.6 + - - -
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Residues in contact with ARG 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E ARG 2.9 18.1 + - - +
51E GLU* 3.8 22.1 + - - +
53E ARG* 1.3 77.4 - - - +
55E TYR* 1.3 108.1 + - + +
57E LYS* 3.1 23.2 + - - +
58E SER* 3.3 19.0 + - - +
8I T 5.2 9.2 - - - +
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Residues in contact with TYR 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E GLU* 2.9 41.7 + - + +
52E ILE 4.4 0.9 - - - +
54E ARG* 1.3 117.7 + - + +
56E GLN* 1.3 58.5 + - - +
58E SER* 3.0 27.0 - - - +
62E LEU* 3.8 20.6 - - + -
37F ARG* 3.0 46.0 - - + +
40F ARG* 4.3 10.3 - - + -
41F ARG* 3.4 35.8 + - + +
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Residues in contact with GLN 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ARG* 2.8 24.6 + - - -
108C VAL* 3.8 16.7 + - + +
109C LEU 3.9 5.4 + - - +
110C PRO* 3.3 29.4 - - + +
111C ASN 3.0 33.0 + - - +
112C ILE* 3.6 14.2 - - - +
52E ILE* 2.9 35.2 + - + +
53E ARG* 4.1 3.8 - - - +
55E TYR* 1.3 77.9 - - - +
57E LYS* 1.3 59.2 + - - +
58E SER 4.2 1.0 - - - +
106E GLU* 5.7 1.6 + - - -
41F ARG* 3.4 30.4 + - - +
42F GLY 5.0 0.4 - - - -
43F GLY* 4.5 4.0 - - - +
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Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ARG* 3.6 18.7 + - - +
110C PRO* 5.6 3.6 - - + -
53E ARG 3.0 17.4 + - - +
54E ARG* 3.1 13.7 + - - +
56E GLN* 1.3 80.5 - - - +
58E SER* 1.3 63.2 + - - +
59E THR* 4.9 0.9 - - - +
8I T 5.3 2.8 - - - -
9I C 4.0 25.7 + - - +
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Residues in contact with SER 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ARG* 4.8 2.6 + - - -
107C GLY* 5.1 0.2 - - - -
54E ARG* 3.3 18.1 + - - +
55E TYR* 3.0 21.7 - - - +
56E GLN 3.4 3.0 - - - +
57E LYS* 1.3 83.3 - - - +
59E THR* 1.3 68.2 + - - +
60E GLU* 3.8 7.9 - - - -
41F ARG* 3.3 10.4 + - - -
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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