Contacts of the strand formed by residues 45 - 51 (chain F) in PDB entry 5GJQ
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ILE 3.9 0.7 - - - +
42F THR* 2.7 45.4 + - - +
43F SER 3.4 0.6 - - - -
44F GLU* 1.3 75.4 - - - +
46F VAL* 1.3 62.9 + - - -
151F PRO* 4.0 9.6 - - - +
191F LEU* 4.1 10.1 - - - +
220F VAL 3.1 15.0 - - - -
221F GLN* 4.1 2.9 - - - -
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Residues in contact with VAL 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F ILE 3.3 11.2 - - - +
41F GLN* 4.2 8.1 - - - -
45F GLY* 1.3 79.3 - - - +
47F CYS* 1.3 68.5 + - - +
48F LEU* 4.6 5.2 - - + +
144F GLY* 4.1 24.2 - - - -
145F GLY 3.9 8.1 - - - +
146F VAL* 5.3 0.2 - - + -
151F PRO* 3.8 18.8 - - + -
152F GLN 3.6 22.7 - - - +
153F LEU* 4.1 18.4 - - + -
191F LEU* 4.5 1.8 - - - +
218F ALA 4.0 0.2 - - - +
219F THR* 3.3 4.1 - - - -
220F VAL* 2.9 37.3 + - + +
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Residues in contact with CYS 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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38F ILE 3.8 0.4 - - - +
39F GLY* 3.2 5.0 - - - -
40F ILE* 2.9 55.6 + - - -
45F GLY 4.3 0.4 + - - -
46F VAL* 1.3 74.9 - - - +
48F LEU* 1.3 64.1 + - - +
191F LEU* 4.2 5.3 - - + +
194F ALA* 3.9 19.7 - - - -
195F ILE* 4.1 20.9 - - + -
198F SER* 3.6 20.9 - - - -
217F LEU* 4.9 4.0 - - + -
218F ALA 3.4 7.4 - - - +
219F THR* 4.1 6.3 - - + -
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ILE 3.5 2.2 - - - +
39F GLY* 4.1 10.1 - - - -
46F VAL* 4.6 4.9 - - + +
47F CYS* 1.3 81.9 - - - +
49F ALA* 1.3 59.9 + - - +
67F ILE* 3.4 17.8 - - + +
75F GLY* 4.1 30.5 - - - +
76F CYS* 4.2 6.5 - - - +
77F ALA* 4.2 7.6 - - + -
142F LEU* 4.0 31.0 - - + +
144F GLY* 4.5 10.1 - - - +
153F LEU* 4.2 11.2 - - + -
217F LEU* 3.2 6.2 - - - +
218F ALA 2.8 39.8 + - - +
220F VAL* 5.4 4.5 - - + -
226F PHE* 4.7 11.2 - - + -
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Residues in contact with ALA 49 (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 ALA* 3.4 1.6 - - - +
38F ILE* 2.8 39.4 + - + +
48F LEU* 1.3 75.4 - - - +
50F VAL* 1.3 65.7 + - - +
67F ILE* 4.2 1.6 - - - -
77F ALA* 5.3 1.7 - - - +
198F SER* 4.3 17.2 - - - -
199F LEU* 4.7 4.0 - - + -
202F LEU* 4.0 18.2 - - + +
215F ILE* 5.3 0.4 - - + -
216F GLU 3.3 7.2 - - - +
217F LEU* 3.6 19.1 - - + -
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Residues in contact with VAL 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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35F SER 4.3 3.6 - - - +
36F THR 3.3 18.6 - - - +
37F ALA* 3.7 13.7 - - + -
49F ALA* 1.3 77.4 - - - +
51F GLU* 1.3 71.2 + - - +
52F LYS* 5.6 0.2 - - + -
66F LYS* 3.5 39.7 - - + +
67F ILE* 3.7 13.9 - - + -
77F ALA* 5.2 1.3 - - + -
78F MET 4.3 6.7 - - - +
202F LEU* 4.0 6.7 - - - -
215F ILE* 3.2 2.9 - - - +
216F GLU* 2.9 52.2 + - + +
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Residues in contact with GLU 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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35F SER* 3.5 25.4 - - - -
36F THR* 3.3 31.4 + - + +
50F VAL* 1.3 80.3 - - - +
52F LYS* 1.3 61.0 + - - +
53F ARG* 3.9 34.4 + - + +
66F LYS* 3.7 2.8 - - - +
172F SER* 4.9 0.5 + - - -
202F LEU* 4.1 5.3 - - + +
205F VAL 5.1 1.0 - - - +
206F MET* 3.3 50.9 - - + +
207F GLU* 4.3 9.6 + - - +
208F GLU 5.5 0.5 + - - -
215F ILE* 3.8 8.3 - - + -
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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