Contacts of the strand formed by residues 14 - 20 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ILE* 1.3 94.0 - - - +
15C ALA* 1.3 55.9 - - - +
16C ASP* 3.9 4.7 - - - +
40C PHE* 3.8 4.7 - - - +
41C GLY 2.8 34.3 + - - +
42C GLY* 3.5 5.1 - - - +
95C THR* 4.6 2.0 - - - -
96C GLY* 3.0 20.0 - - - +
97C VAL 3.7 4.4 + - - -
98C ALA* 4.1 10.8 - - - +
112C ILE* 4.4 12.6 - - - +
113C HIS 4.5 1.4 - - - +
117C ASN* 2.9 16.4 + - - +
143C GLU* 3.9 7.5 + - - -
1312C RIB 3.1 40.7 + - - +
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Residues in contact with ALA 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ASN* 1.3 71.0 - - - +
16C ASP* 1.3 61.3 + - - +
17C HIS* 3.3 22.9 - - + +
38C VAL* 5.0 4.3 - - + -
39C ALA 3.7 6.5 - - - +
40C PHE* 4.9 4.0 - - + +
69C ILE* 4.0 31.0 - - + -
95C THR* 4.5 4.2 - - + +
96C GLY 2.9 11.3 + - - +
97C VAL* 3.7 7.4 - - + -
98C ALA 3.2 18.2 + - - -
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Residues in contact with ASP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASN* 3.9 1.2 - - - +
15C ALA* 1.3 72.9 - - - +
17C HIS* 1.3 60.7 + - - +
18C ILE* 3.7 20.7 - - + +
37C GLN 3.5 1.4 - - - +
38C VAL* 3.1 8.5 - - - +
39C ALA 2.5 40.1 + - - +
40C PHE 4.0 0.2 - - - +
41C GLY* 3.2 15.3 + - - -
98C ALA* 3.2 13.7 - - - +
100C ILE* 3.8 12.3 - - + +
291C ALA* 3.7 11.8 - - - +
1312C RIB 2.6 45.7 + - - -
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Residues in contact with HIS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA* 3.3 26.8 + - - +
16C ASP* 1.3 75.4 - - - +
18C ILE* 1.3 59.4 + - - +
36C TYR* 3.0 26.4 + - - +
37C GLN 3.6 3.8 - - - -
38C VAL* 3.9 18.4 - - + +
97C VAL* 4.1 12.4 - - + +
98C ALA 2.9 15.9 + - - +
99C LEU* 4.1 13.2 - - + -
100C ILE 2.9 27.7 + - - +
17D HIS* 3.7 30.4 + + - -
36D TYR* 4.9 1.3 + - - -
99D LEU* 3.6 14.1 - - + +
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Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ASP* 3.7 26.5 - - + +
17C HIS* 1.3 76.8 - - - +
19C LEU* 1.3 64.1 + - - +
20C ASN* 4.8 9.1 + - - +
35C HIS 3.8 0.7 - - - +
36C TYR* 3.3 9.3 - - - -
37C GLN* 2.8 55.5 + - + +
39C ALA* 4.8 7.0 - - + -
100C ILE* 3.4 24.0 - - + +
102C VAL* 3.9 26.7 - - + -
249C ASP* 5.2 2.2 - - - +
251C ILE* 4.0 10.5 - - + -
289C LYS* 6.1 1.1 - - - -
290C GLY* 4.2 24.2 - - - +
291C ALA 4.6 2.5 - - - +
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 1.3 73.6 - - - +
20C ASN* 1.3 67.2 + - - +
21C LEU* 3.6 16.3 + - + +
33C GLY* 4.3 9.9 - - - +
35C HIS 3.3 20.6 - - - +
36C TYR* 4.1 5.8 - - + -
100C ILE 2.8 11.3 + - - +
101C PHE* 3.5 10.7 - - + -
102C VAL 3.0 22.3 + - - -
99D LEU* 3.9 18.4 - - + -
111D GLY* 3.4 39.3 - - - +
112D ILE 3.4 19.5 - - - +
113D HIS* 4.1 18.6 - - + +
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Residues in contact with ASN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 4.8 9.5 + - - +
19C LEU* 1.3 71.3 - - - +
21C LEU* 1.3 56.0 + - - +
33C GLY* 3.0 6.2 - - - -
34C ASN* 2.7 45.9 + - - +
35C HIS* 2.8 51.3 + - + +
37C GLN* 5.5 0.4 - - - +
102C VAL* 3.3 20.5 - - - +
103C ASN 4.9 1.2 - - - +
289C LYS* 2.6 36.6 + - - +
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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