Contacts of the helix formed by residues 30 - 42 (chain F) in PDB entry 5X0X
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 THR 30 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F GLN 3.7 8.5 - - - +
28F GLY* 3.1 18.8 + - - +
29F ILE* 1.3 77.6 - - - +
31F LYS* 1.3 55.6 + - - +
32F PRO* 3.5 15.0 - - - +
33F ALA* 2.6 45.5 + - - +
34F ILE* 2.9 14.5 + - - +
55F ARG* 4.6 1.1 - - - +
61I A 4.2 17.6 + - - +
62I C 3.9 19.1 - - - +
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Residues in contact with LYS 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F ILE 4.3 0.6 + - - -
30F THR* 1.3 70.4 - - - +
32F PRO* 1.3 70.1 - - + +
34F ILE* 4.7 2.5 - - - -
35F ARG* 2.9 39.6 + - + +
51F TYR* 3.3 58.2 - - + +
55F ARG* 4.3 9.1 - - - +
62I C 4.6 2.9 + - - +
82J G 5.8 2.9 + - - -
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Residues in contact with PRO 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F THR* 3.3 7.9 - - - +
31F LYS* 1.3 93.0 - - + +
33F ALA* 1.3 57.1 + - - +
35F ARG* 3.2 9.2 - - + +
36F ARG* 2.9 33.4 + - - +
61I A 3.4 41.7 - - + +
62I C 3.0 30.3 - - + +
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Residues in contact with ALA 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E LEU 3.8 10.5 - - - +
62E ILE* 4.8 14.8 - - + -
63E ARG* 5.7 1.8 - - + +
29F ILE* 5.1 3.1 - - + -
30F THR* 2.6 29.8 + - - +
32F PRO* 1.3 70.3 - - - +
34F ILE* 1.3 59.9 + - + +
36F ARG* 2.5 50.8 + - - +
37F LEU* 2.9 15.2 + - - +
61I A 4.9 0.2 - - - +
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Residues in contact with ILE 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 4.4 11.0 - - + -
29F ILE* 3.5 32.1 - - + -
30F THR 2.9 14.8 + - - +
31F LYS 4.3 2.2 - - - +
33F ALA* 1.3 74.2 - - - +
35F ARG* 1.3 63.0 + - - +
37F LEU* 3.3 13.7 + - + +
38F ALA* 2.9 22.9 + - + +
46F ILE* 5.8 0.7 - - + -
50F ILE* 5.2 1.8 - - + -
51F TYR* 4.0 44.0 - - + +
54F THR* 4.0 34.8 - - + +
55F ARG* 4.4 12.8 - - + +
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Residues in contact with ARG 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLU* 4.7 10.3 + - - +
31F LYS* 2.9 35.9 + - - +
32F PRO* 3.2 9.0 - - - +
34F ILE* 1.3 78.3 - - - +
36F ARG* 1.3 62.8 + - + +
38F ALA* 3.2 4.9 + - - +
39F ARG* 2.9 56.4 + - + +
46F ILE* 3.6 25.7 - - + +
51F TYR* 4.5 8.0 + - - +
82J G 4.0 38.9 + - - +
83J T 4.1 22.0 + - - +
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Residues in contact with ARG 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLU* 6.6 0.4 - - - -
54E TYR* 3.2 43.3 - - + +
61E LEU* 3.3 35.5 + - + +
63E ARG* 3.1 26.9 - - - +
32F PRO* 2.9 17.9 + - - +
33F ALA* 2.5 26.0 + - - +
35F ARG* 1.3 71.2 - - + +
37F LEU* 1.3 55.3 + - - +
39F ARG* 2.7 32.1 + - + +
40F ARG* 2.9 11.4 + - - +
60I A 4.8 4.2 - - - -
61I A 2.5 45.9 + - - -
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Residues in contact with LEU 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E LEU* 3.6 35.7 - - + -
62E ILE* 4.4 19.5 - - + -
97E GLU* 4.0 21.5 - - + -
100E LEU* 3.9 31.9 - - + -
101E VAL* 4.4 18.9 - - + +
104E PHE* 4.2 11.9 - - + -
29F ILE* 6.1 1.3 - - + -
33F ALA* 2.9 12.6 + - + +
34F ILE* 3.6 19.7 - - + +
36F ARG* 1.3 72.5 - - - +
38F ALA* 1.3 65.3 + - - +
40F ARG* 3.0 6.0 + - - +
41F GLY* 2.9 19.4 + - - -
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Residues in contact with ALA 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 3.5 23.1 - - + -
119E ILE* 5.5 1.1 - - + -
34F ILE* 2.9 13.6 + - + +
35F ARG 3.3 10.3 - - - +
37F LEU* 1.3 74.1 - - - +
39F ARG* 1.3 63.9 + - + +
41F GLY 3.0 10.2 + - - -
43F VAL* 3.0 42.0 + - + +
46F ILE* 3.8 20.9 - - + -
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Residues in contact with ARG 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ALA* 3.3 22.7 - - - +
50E GLU* 3.1 32.0 + - + +
51E ILE* 3.6 22.1 - - + +
54E TYR* 4.3 18.8 - - + -
35F ARG* 2.9 55.6 + - + +
36F ARG* 2.7 16.5 + - - +
38F ALA* 1.3 71.3 - - - +
40F ARG* 1.3 55.0 + - - +
42F GLY* 2.6 27.5 + - - -
43F VAL* 3.4 13.4 + - - +
44F LYS 2.2 39.8 + - - -
46F ILE* 4.7 9.9 - - - +
82J G 4.6 11.3 + - - -
83J T 5.4 0.2 + - - -
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Residues in contact with ARG 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLY* 4.8 9.5 - - - +
107C VAL* 4.0 34.2 - - + +
54E TYR* 4.0 31.8 + - + +
55E GLN* 3.4 21.6 + - - +
57E SER 3.5 21.0 + - - -
58E THR* 3.8 7.2 + - - -
59E GLU* 2.7 34.1 + - - +
60E LEU* 5.6 1.4 - - - +
61E LEU* 3.3 32.8 - - + +
97E GLU* 4.8 9.7 + - - +
101E VAL* 4.1 17.6 - - + +
36F ARG 2.9 10.3 + - - +
37F LEU* 3.5 7.6 - - - +
39F ARG* 1.3 75.1 - - - +
41F GLY* 1.3 62.9 + - - +
42F GLY 3.1 1.0 + - - -
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Residues in contact with GLY 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ASN 5.2 0.2 - - - +
55E GLN* 4.1 4.7 + - - -
101E VAL* 4.1 22.4 - - - +
104E PHE* 4.8 3.4 - - - -
105E GLU* 3.4 34.6 - - - +
108E ASN* 5.4 1.0 + - - -
37F LEU 2.9 14.1 + - - -
38F ALA 3.0 5.1 + - - -
40F ARG* 1.3 77.7 - - - +
42F GLY* 1.3 59.8 + - - +
43F VAL* 3.5 1.1 - - - -
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Residues in contact with GLY 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ASN 4.8 3.1 - - - -
111C ILE* 5.7 2.6 - - - +
115C LEU* 3.6 13.0 - - - +
51E ILE* 3.9 11.0 - - - +
55E GLN* 4.0 12.6 - - - -
108E ASN* 3.3 20.2 + - - -
39F ARG 2.6 20.5 + - - -
40F ARG 3.1 0.8 + - - -
41F GLY* 1.3 73.8 - - - -
43F VAL* 1.3 65.1 + - - +
44F LYS 3.5 1.0 + - - -
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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