Contacts of the strand formed by residues 52 - 58 (chain A) in PDB entry 1GTN
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLY* 3.9 11.0 - - - -
24A LEU 3.3 6.5 - - - +
26A ARG* 3.8 0.9 + - - -
33A HIS* 2.9 16.8 + - - -
47A GLN 4.6 1.1 - - - +
48A PHE* 3.6 5.2 - - - -
49A THR* 2.9 38.9 + - - +
51A HIS* 1.3 75.4 - - - +
53A SER* 1.3 59.9 + - - +
54A ALA 3.4 23.3 - - - +
55A ILE* 3.9 19.3 - - + -
81A TRP* 2.7 32.8 + - + +
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU 3.3 4.6 + - - -
25A THR 3.9 0.7 + - - -
26A ARG* 3.6 34.5 - - - +
48A PHE* 3.9 5.4 - - - -
51A HIS 4.2 0.8 + - - -
52A THR* 1.3 73.7 - - - +
54A ALA* 1.3 60.3 + - - +
47B GLN* 3.1 36.5 + - - +
49B THR* 3.9 5.8 - - - -
81B TRP* 2.9 40.7 + - - +
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 2.9 53.3 + - + -
48A PHE* 3.9 1.1 - - - -
52A THR* 3.4 7.7 - - - +
53A SER* 1.3 81.4 + - - +
55A ILE* 1.3 64.4 + - - +
44B LEU* 4.5 5.2 - - + -
45B ILE 3.1 14.1 - - - +
46B ALA* 3.9 14.1 - - + -
81B TRP* 4.3 10.3 - - + -
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.1 15.7 - - + -
12A ILE* 5.1 4.0 - - + -
21A VAL* 3.8 26.5 - - + -
22A ILE 3.3 9.2 - - - +
46A ALA* 4.4 8.5 - - + +
47A GLN 4.2 9.4 - - - +
48A PHE* 3.6 27.8 - - + -
52A THR* 3.9 4.5 - - + -
54A ALA* 1.3 80.3 - - - +
56A LYS* 1.3 66.5 + - - +
57A VAL* 4.6 2.7 - - + -
81A TRP* 3.8 26.2 - - + -
44B LEU* 3.5 5.2 - - - +
45B ILE* 2.7 54.9 + - + +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASN 3.5 1.7 - - - +
21A VAL* 3.6 1.7 - - - -
22A ILE* 2.8 51.1 + - + +
24A LEU* 4.3 7.3 - - + +
32A PHE* 4.0 15.2 - - + -
55A ILE* 1.3 75.3 - - - +
57A VAL* 1.3 71.5 + - - +
58A ARG* 4.0 22.8 - - + +
36B GLU* 2.8 30.5 + - - -
37B LYS 3.3 16.4 + - - -
38B LEU* 3.2 26.0 - - + -
42B GLU* 4.1 10.5 + - + +
43B VAL 3.4 11.2 - - - +
44B LEU* 3.9 11.2 - - + -
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 4.0 21.8 - - + -
19A VAL* 4.2 17.3 - - + -
20A ASN 3.3 9.2 - - - +
21A VAL* 4.7 2.7 - - + -
55A ILE* 4.6 5.6 - - + -
56A LYS* 1.3 79.8 - - - +
58A ARG* 1.3 62.0 + - - +
59A GLY 4.2 1.9 + - - +
61A ALA* 4.2 6.1 - - + -
63A ILE* 3.9 24.5 - - + -
72A SER* 3.6 22.9 - - - +
42B GLU* 3.8 7.1 - - - +
43B VAL* 2.8 33.5 + - + +
45B ILE* 4.5 13.7 - - + -
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLY 4.5 0.7 - - - +
19A VAL* 3.6 5.0 - - - +
20A ASN* 2.9 55.0 + - + +
22A ILE* 3.8 21.1 - - + +
32A PHE* 4.6 13.5 - - - -
56A LYS* 4.0 29.1 - - + +
57A VAL* 1.3 75.0 - - - +
59A GLY* 1.3 62.8 + - - +
42B GLU* 3.3 32.7 + - + +
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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