Contacts of the helix formed by residues 42 - 52 (chain F) in PDB entry 2GTL
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 PRO 42 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F PHE* 3.0 17.1 - - - +
39F ALA 4.1 5.8 - - - +
40F GLN 3.5 8.3 - - - +
41F VAL* 1.3 85.7 - - - +
43F GLU* 1.3 70.2 + - + +
45F ARG* 3.1 33.5 + - - +
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Residues in contact with GLU 43 (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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41F VAL* 2.8 5.7 + - + +
42F PRO* 1.3 86.7 - - + +
44F SER* 1.3 59.0 + - - +
45F ARG 3.2 1.2 + - - -
46F SER* 3.0 24.9 + - - -
104F ASN* 6.3 0.2 - - - +
105F TYR* 3.3 22.2 + - + +
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Residues in contact with SER 44 (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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37F THR* 4.6 0.7 - - - +
38F PHE* 3.4 16.2 - - - -
41F VAL* 2.7 31.4 + - - +
43F GLU* 1.3 74.6 - - - +
45F ARG* 1.3 66.0 + - - +
46F SER 3.0 3.1 - - - -
47F LEU* 3.0 15.5 + - - +
48F PHE* 3.3 13.7 - - - -
105F TYR* 3.3 38.4 + - - -
160F HEM 4.0 11.1 - - - +
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Residues in contact with ARG 45 (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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35F ARG* 6.0 1.8 - - - +
38F PHE* 3.7 55.6 + - + +
39F ALA* 5.8 0.4 - - - +
42F PRO* 3.1 24.9 + - - +
44F SER* 1.3 79.8 + - - +
46F SER* 1.3 62.8 + - - +
47F LEU 3.1 1.4 + - - -
48F PHE* 3.1 15.2 + - - +
49F LYS* 3.7 8.8 + - - +
53F GLY* 3.2 28.5 + - - +
54F ASP* 4.0 13.9 + - - +
56F THR* 3.9 24.7 - - - +
86N HIS* 5.3 7.9 - - - -
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Residues in contact with SER 46 (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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42F PRO 4.6 0.2 + - - -
43F GLU 3.0 17.8 + - - -
45F ARG* 1.3 79.8 - - - +
47F LEU* 1.3 72.2 + - - +
49F LYS* 3.5 23.6 - - - +
105F TYR* 5.2 0.2 + - - -
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Residues in contact with LEU 47 (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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44F SER* 3.0 11.5 + - - +
46F SER* 1.3 93.4 - - - +
48F PHE* 1.3 65.5 + - + +
49F LYS 3.2 3.3 + - - -
50F ARG* 4.6 5.2 + - - +
99F ARG* 5.4 6.3 + - + -
100F LYS 4.7 9.9 - - - +
101F ILE* 4.1 17.7 - - + -
105F TYR* 3.9 31.2 - - + +
160F HEM 3.6 44.7 - - + +
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Residues in contact with PHE 48 (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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34F TRP* 3.5 14.4 - + - -
38F PHE* 3.6 24.5 - + - -
44F SER 3.3 21.5 - - - -
45F ARG 3.1 8.3 + - - +
47F LEU* 1.3 80.3 - - + +
49F LYS* 1.3 62.0 + - - +
50F ARG* 3.0 2.9 - - - +
51F VAL* 3.2 20.5 + - + -
53F GLY* 2.8 30.6 + - - -
61F PHE* 4.6 3.4 - + + -
64F HIS* 3.2 35.0 - + - -
160F HEM 3.4 66.9 - - + -
161F CMO 3.6 3.8 - - - -
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Residues in contact with LYS 49 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45F ARG 3.7 5.5 + - - +
46F SER* 3.5 20.3 + - - +
47F LEU 3.2 2.8 - - - -
48F PHE* 1.3 79.3 - - - +
50F ARG* 1.3 61.7 + - - +
51F VAL 3.4 0.3 + - - -
52F HIS* 3.6 10.2 + - - -
53F GLY 4.5 2.7 - - - +
54F ASP* 4.6 25.8 - - + +
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Residues in contact with ARG 50 (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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47F LEU 4.6 4.6 + - - +
48F PHE 3.0 0.9 - - - -
49F LYS* 1.3 81.2 - - - +
51F VAL* 1.3 63.3 + - - +
52F HIS* 3.5 7.0 + - - -
67F ARG* 4.9 3.4 - - - +
160F HEM 3.4 35.5 + - - +
97G HIS* 3.5 32.3 + - - -
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Residues in contact with VAL 51 (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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48F PHE* 3.7 25.4 - - + +
50F ARG* 1.3 85.8 - - - +
52F HIS* 1.3 72.6 + - - +
53F GLY 3.2 0.6 + - - -
60F ALA* 3.2 34.5 - - + +
61F PHE* 3.4 8.9 - - + +
64F HIS* 3.4 35.7 - - + +
67F ARG* 4.4 6.7 - - - +
160F HEM 4.3 16.8 - - + +
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Residues in contact with HIS 52 (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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48F PHE 3.6 0.6 + - - -
49F LYS 3.6 6.0 + - - -
50F ARG 3.5 7.2 + - - -
51F VAL* 1.3 79.0 - - - +
53F GLY* 1.3 64.0 + - - +
54F ASP* 3.1 24.0 - - - +
55F ASP* 3.3 17.1 - - + +
58F HIS* 3.2 53.4 + + + +
60F ALA* 3.8 12.2 - - + +
61F PHE* 3.4 6.5 - - - +
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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