Contacts of the helix formed by residues 43 - 54 (chain B) in PDB entry 2G5W
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 43 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ARG 3.0 24.2 + - - +
37B ALA* 3.9 1.4 - - - +
38B LEU* 3.9 13.7 - - - +
41B VAL 3.8 12.1 + - - +
42B PRO* 1.3 75.5 - - - +
44B ALA* 1.3 63.1 + - - +
45B ALA* 3.1 27.4 + - - +
46B LEU* 3.3 15.5 + - - +
47B ALA* 3.2 18.0 + - - +
91B GLN* 3.4 15.7 + - - +
92B VAL* 3.9 3.1 - - - +
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Residues in contact with ALA 44 (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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43B ASN* 1.3 74.6 - - - +
45B ALA* 1.3 60.0 + - - +
46B LEU 3.4 0.2 - - - -
47B ALA* 3.3 6.1 + - + +
48B GLU* 2.9 29.3 + - - +
91B GLN* 3.6 19.6 - - - +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 5.4 2.5 - - + +
43B ASN* 3.1 12.0 + - - +
44B ALA* 1.3 75.2 - - - +
46B LEU* 1.3 64.9 + - + +
48B GLU* 3.4 7.4 + - - +
49B TYR* 2.9 24.8 + - - +
375B PRO* 3.7 42.8 - - + +
379B TYR* 3.5 10.1 - - + -
380B THR* 4.2 1.4 - - - +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 3.6 36.3 - - + +
37B ALA* 3.7 18.2 - - + +
42B PRO* 4.2 13.2 - - + -
43B ASN* 3.3 19.3 + - - +
44B ALA 3.4 0.2 - - - -
45B ALA* 1.3 78.2 - - - +
47B ALA* 1.3 64.0 + - - +
49B TYR* 3.1 2.6 + - - +
50B TYR* 2.9 33.1 + - + -
63B GLU* 3.6 27.1 - - - +
78B PRO* 4.3 0.2 - - + -
89B TRP* 4.1 22.4 - - + -
92B VAL* 4.0 5.6 - - + -
379B TYR* 3.5 24.2 - - - +
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASN 3.2 10.4 + - - +
44B ALA* 3.4 13.2 - - - +
45B ALA 3.3 0.2 - - - -
46B LEU* 1.3 78.5 - - - +
48B GLU* 1.3 57.4 + - - +
50B TYR* 4.0 1.4 - - - +
51B ALA* 3.0 31.5 + - - +
91B GLN* 4.0 13.2 - - + +
92B VAL* 3.7 35.3 - - - +
95B ALA* 3.9 8.8 - - + +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA 2.9 17.1 + - - +
45B ALA* 3.7 6.1 - - - +
46B LEU 3.2 0.2 - - - -
47B ALA* 1.3 76.1 - - - +
49B TYR* 1.3 56.7 + - - +
51B ALA* 3.3 7.4 + - - +
52B GLN* 2.9 58.3 + - - +
380B THR* 3.6 22.4 - - + +
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Residues in contact with TYR 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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29B LEU* 4.9 3.9 - - + +
32B MET* 4.2 19.7 - - - +
34B ARG* 3.4 42.0 + - + +
45B ALA 2.9 18.0 + - - +
46B LEU 3.4 2.2 - - - +
48B GLU* 1.3 76.9 - - - +
50B TYR* 1.3 96.6 + + - +
52B GLN* 3.6 3.0 - - - +
53B ARG* 3.1 66.9 + - - +
63B GLU* 4.9 0.2 - - - -
347B ILE* 4.6 1.4 - - - +
379B TYR* 3.3 53.2 - + + -
380B THR* 3.7 10.5 - - + -
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Residues in contact with TYR 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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29B LEU* 3.8 28.9 - - + -
32B MET 4.7 1.7 + - - -
46B LEU* 2.9 34.2 + - + +
47B ALA 4.1 2.0 - - - +
49B TYR* 1.3 93.1 - + - +
51B ALA* 1.3 57.3 + - - +
53B ARG* 2.8 25.2 + - - +
54B THR* 2.9 17.6 + - - +
60B LEU* 4.2 3.9 - - + +
61B ILE 4.4 0.7 - - - -
62B SER* 3.5 17.1 - - - -
63B GLU* 2.7 54.7 + - - +
89B TRP* 4.8 4.0 - + - -
92B VAL* 3.8 22.2 - - + -
96B VAL* 4.0 16.4 - - + -
103B ILE* 4.0 14.1 - - + -
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Residues in contact with ALA 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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47B ALA 3.0 20.1 + - - +
48B GLU* 3.6 10.8 - - - +
50B TYR* 1.3 75.5 - - - +
52B GLN* 1.3 61.8 - - - +
53B ARG 3.2 0.7 + - - -
54B THR* 3.3 17.7 + - - +
95B ALA* 3.9 26.5 - - + +
96B VAL* 4.5 1.0 - - - +
99B LYS* 3.3 33.5 + - + +
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Residues in contact with GLN 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 GLU* 2.9 48.4 + - - +
49B TYR 3.6 6.5 - - - +
51B ALA* 1.3 76.2 - - - +
53B ARG* 1.3 79.3 + - - +
54B THR 3.9 3.5 + - - +
99B LYS* 5.3 3.8 + - - +
350B PRO* 3.4 17.1 - - + +
380B THR* 3.3 38.2 + - - +
382B TYR* 4.9 1.0 - - - +
384B PHE* 3.5 42.9 - - + -
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Residues in contact with ARG 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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29B LEU* 4.4 19.1 - - + -
49B TYR* 3.1 56.0 + - - +
50B TYR 2.8 9.4 + - - +
52B GLN* 1.3 106.6 + - - +
54B THR* 1.3 61.6 + - - +
55B THR* 3.9 5.5 + - - +
60B LEU* 3.5 12.2 - - - +
346B PHE* 3.0 44.8 + - + -
347B ILE 2.7 28.9 + - - -
350B PRO* 3.5 33.7 - - + +
353B VAL* 6.0 0.2 - - - +
379B TYR 3.7 12.9 + - - -
380B THR* 5.4 0.2 - - - +
382B TYR* 4.4 4.2 - - - +
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Residues in contact with THR 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 TYR 2.9 18.4 - - - +
51B ALA* 3.3 20.8 + - - +
52B GLN 4.5 3.1 - - - +
53B ARG* 1.3 79.2 - - - +
55B THR* 1.3 64.9 + - - +
56B PRO* 4.9 0.3 - - - +
58B GLY 5.9 0.2 - - - -
60B LEU* 3.5 27.1 - - + -
96B VAL* 3.6 25.7 + - + -
99B LYS* 3.1 36.4 + - - +
101B GLY* 4.6 5.2 - - - -
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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