Contacts of the strand formed by residues 48 - 53 (chain F) in PDB entry 1GLE
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 ASP 48 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ILE* 3.5 5.7 - - - +
44F LYS* 3.3 42.5 + - + +
47F GLY* 1.3 75.7 - - - -
49F GLY* 1.3 72.7 + - - +
139F VAL* 3.6 6.3 - - - -
140F ILE* 2.5 43.7 + - - +
143F MET* 3.6 28.1 - - + +
149F LEU* 4.2 11.4 - - + +
151F LYS* 3.4 14.1 + - - -
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Residues in contact with GLY 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F ILE* 3.4 12.9 - - - +
48F ASP* 1.3 84.7 + - - +
50F ILE* 1.3 63.4 + - - -
138F VAL 3.2 12.1 - - - -
139F VAL* 3.9 0.2 - - - -
149F LEU* 4.9 2.0 - - - -
151F LYS* 3.2 27.9 + - - -
164F ILE* 3.7 16.6 - - - -
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Residues in contact with ILE 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ILE* 3.6 17.3 - - + -
31F VAL 3.2 18.8 - - - +
32F ASN* 5.1 3.6 - - - +
33F ILE* 4.8 6.2 - - - +
49F GLY* 1.3 75.5 - - - +
51F ALA* 1.3 65.1 + - - +
52F ILE* 4.2 4.5 - - + -
137F PRO* 3.5 2.9 - - - +
138F VAL* 2.7 50.8 + - + +
139F VAL* 4.8 1.2 - - - +
151F LYS* 4.8 17.7 - - + -
152F LEU 4.7 7.2 - - - +
163F VAL* 3.4 38.1 - - + +
164F ILE* 3.7 20.4 - - + -
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Residues in contact with ALA 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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30F ILE* 3.4 2.4 - - - +
31F VAL* 2.9 38.8 + - + +
32F ASN 5.0 0.4 - - - +
33F ILE* 4.9 3.8 - - + -
36F VAL* 4.1 26.5 - - + -
50F ILE* 1.3 84.0 - - - +
52F ILE* 1.3 75.6 + - - +
135F LEU* 4.9 4.3 - - + -
136F THR 3.7 9.2 - - - +
137F PRO* 4.1 9.6 - - + -
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Residues in contact with ILE 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F PRO* 4.4 7.4 - - + -
26F LEU* 3.2 45.5 - - + +
27F SER 4.0 12.1 - - - +
28F GLY 4.3 0.4 - - - +
29F GLU 3.3 12.6 - - - +
30F ILE* 4.1 9.4 - - + -
31F VAL* 4.5 0.7 - - - +
50F ILE* 4.2 15.9 - - + -
51F ALA* 1.3 88.0 - - - +
53F LYS* 1.3 75.6 + - - +
54F PRO* 3.2 7.7 - - - +
135F LEU* 4.0 3.1 - - - +
136F THR* 2.9 29.9 + - - +
138F VAL* 4.3 10.3 - - + -
156F VAL* 4.7 5.8 - - + -
163F VAL* 4.5 10.5 - - + -
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Residues in contact with LYS 53 (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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28F GLY* 3.0 25.3 - - - -
29F GLU* 2.9 23.0 + - + +
31F VAL* 4.5 7.9 - - + +
52F ILE* 1.3 71.6 - - - +
54F PRO* 1.3 76.9 - - + +
55F THR* 4.9 2.0 - - + +
128F GLU* 4.9 4.3 - - - +
134F THR* 4.1 17.5 - - + -
135F LEU* 3.9 17.0 - - + +
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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