Contacts of the strand formed by residues 14 - 20 (chain D) in PDB entry 1GQT
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 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D SER* 4.8 1.1 - - - -
13D ILE* 1.3 88.4 - - - +
15D ALA* 1.3 56.8 + - - +
16D ASP* 3.5 4.9 - - - +
40D PHE* 3.6 6.4 - - - +
41D GLY 2.7 36.8 + - - +
42D GLY* 3.5 14.7 - - - +
95D THR* 5.0 0.9 - - - -
96D GLY* 3.3 15.3 - - - +
97D VAL 3.8 6.3 + - - -
98D ALA* 4.2 6.6 - - - +
112D ILE* 4.3 12.3 - - - +
113D HIS 4.4 2.9 - - - +
117D ASN* 3.4 13.2 + - - -
143D GLU* 3.8 6.6 + - - -
1310D RIB 2.8 40.2 + - - +
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Residues in contact with ALA 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASN* 1.3 71.4 - - - +
16D ASP* 1.3 57.4 + - - +
17D HIS* 3.5 16.8 - - + +
38D VAL* 5.2 5.8 - - + -
39D ALA 3.9 4.5 - - - -
40D PHE* 4.9 3.8 - - + +
69D ILE* 3.9 32.3 - - + -
95D THR* 4.7 1.6 - - + +
96D GLY 2.7 16.2 + - - +
97D VAL* 3.4 8.8 - - + -
98D ALA 2.7 30.7 + - - +
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Residues in contact with ASP 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASN* 3.5 5.4 + - - +
15D ALA* 1.3 72.3 - - - +
17D HIS* 1.3 61.4 + - - +
18D ILE* 4.0 20.1 - - + +
37D GLN 3.6 1.3 - - - +
38D VAL* 3.0 9.0 - - - +
39D ALA* 2.7 45.7 + - + +
40D PHE 4.8 0.2 - - - -
41D GLY* 3.3 13.5 - - - -
98D ALA* 3.3 13.0 - - - +
100D ILE* 4.1 7.0 - - + +
251D ILE* 5.5 0.3 - - - +
291D ALA* 3.9 9.6 - - + +
1310D RIB 2.6 48.7 + - - -
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Residues in contact with HIS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C HIS* 3.7 29.2 + + - -
36C TYR* 4.8 1.2 + - - -
99C LEU* 3.7 15.3 - - + +
15D ALA* 3.5 26.9 + - + +
16D ASP* 1.3 74.9 - - - +
18D ILE* 1.3 61.1 + - - +
36D TYR* 2.9 29.1 + - + +
37D GLN 3.7 3.4 - - - -
38D VAL* 3.9 16.0 - - + +
97D VAL* 3.9 17.3 - - + +
98D ALA 2.8 15.8 + - - +
99D LEU* 4.2 8.7 - - + -
100D ILE* 2.8 29.3 + - - +
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Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ASP* 4.1 23.3 - - + +
17D HIS* 1.3 77.0 - - - +
19D LEU* 1.3 61.0 + - - +
20D ASN* 4.5 11.0 + - - +
35D HIS 3.7 1.0 - - - +
36D TYR* 3.3 9.9 - - - -
37D GLN* 2.8 61.4 + - + +
39D ALA* 5.2 3.4 - - + -
100D ILE* 3.5 17.3 - - + +
102D VAL* 3.8 27.8 - - + -
251D ILE* 4.3 19.3 - - + -
289D LYS* 5.3 5.4 - - - -
290D GLY* 4.3 12.6 - - - +
291D ALA* 4.8 4.7 - - + +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LEU* 4.1 17.0 - - + -
111C GLY* 3.4 39.7 - - - +
112C ILE 3.5 20.2 - - - +
113C HIS* 3.9 20.0 - - + +
17D HIS 4.0 1.0 + - - -
18D ILE* 1.3 75.2 - - - +
20D ASN* 1.3 65.7 + - - +
21D LEU* 3.7 15.9 + - + +
33D GLY* 3.6 13.7 - - - -
35D HIS 3.6 13.5 - - - +
36D TYR* 4.4 6.3 - - + -
100D ILE 3.0 9.3 + - - +
101D PHE* 3.6 10.6 - - + -
102D VAL 3.2 23.0 + - - -
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Residues in contact with ASN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 4.5 9.3 + - - +
19D LEU* 1.3 74.5 - - - +
21D LEU* 1.3 58.9 + - - +
33D GLY* 3.2 6.4 - - - -
34D ASN* 2.8 46.4 + - - +
35D HIS* 2.9 40.1 + - + +
37D GLN* 5.9 0.8 - - - +
102D VAL* 3.7 17.9 - - - +
289D LYS* 3.0 35.8 + - - +
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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