Contacts of the strand formed by residues 50 - 56 (chain B) in PDB entry 1GCT
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 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ASN* 2.7 13.6 - - - +
49B GLU* 1.3 84.6 + - - +
51B TRP* 1.3 77.8 + - + +
107B LYS* 3.6 18.0 + - - +
108B LEU* 2.9 43.4 + - - +
109B SER 5.6 0.5 - - - +
111B ALA* 3.6 23.1 + - - +
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Residues in contact with TRP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 3.7 3.1 - - - -
47B ILE* 3.0 41.5 + - + -
48B ASN* 3.2 36.6 + - - +
49B GLU 3.6 1.0 - - - -
50B ASN* 1.3 92.9 - - + +
52B VAL* 1.3 64.1 + - - +
89B PHE* 3.4 40.6 - + - -
105B LEU* 4.0 17.7 - - + -
106B LEU 3.3 19.5 - - - -
107B LYS* 3.0 32.5 - - + +
108B LEU* 4.2 1.4 - - - +
241C THR* 4.3 7.2 - - + -
242C LEU* 3.6 34.4 + - + +
245C ASN* 3.6 29.0 + - + -
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 3.8 22.4 - - + -
33B LEU* 5.0 0.7 - - + -
44B GLY* 4.1 3.4 - - - -
45B SER 3.5 7.4 - - - +
46B LEU* 3.8 21.3 - - + -
47B ILE* 5.1 0.2 - - - -
51B TRP* 1.3 77.7 - - - +
53B VAL* 1.3 77.3 + - - +
54B THR* 4.8 1.1 - - - -
66B VAL* 4.1 20.4 - - + -
104B THR 4.0 0.2 - - - +
105B LEU* 3.5 4.6 - - - +
106B LEU* 2.7 62.1 + - + +
108B LEU* 4.2 12.6 - - + -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLY* 3.3 3.8 - - - -
45B SER* 2.9 45.2 + - - +
47B ILE* 3.9 20.6 - - + +
52B VAL* 1.3 72.8 - - - +
54B THR* 1.3 61.0 + - - +
103B ILE* 4.7 9.9 - - + -
104B THR 3.6 5.8 - - - +
105B LEU* 3.2 27.4 - - + -
123B LEU* 5.3 1.8 - - + -
196C GLY 3.9 1.9 - - - +
209C LEU* 3.5 31.0 - - + -
212C ILE* 4.5 16.4 - - + -
238C VAL* 4.9 5.2 - - + -
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Residues in contact with THR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.5 17.1 - - + +
43B GLY 2.8 24.3 + - - -
44B GLY* 4.3 1.8 - - - -
53B VAL* 1.3 75.0 - - - +
55B ALA* 1.3 73.1 + - - +
58B CYS* 3.9 5.0 - - - -
60B VAL* 4.4 6.1 - - + -
103B ILE* 3.4 10.0 - - - +
104B THR* 3.0 42.1 + - + +
106B LEU* 4.1 22.9 - - + -
196C GLY* 3.4 10.9 - - - -
212C ILE* 4.0 9.6 - - - +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B THR* 1.3 86.1 + - - +
56B ALA* 1.3 64.4 + - - +
57B HIS* 3.8 13.5 - - + +
58B CYS* 3.3 21.1 + - - +
59B GLY 4.6 0.3 + - - -
60B VAL* 5.4 0.3 - - - +
102B ASP* 3.5 28.3 - - - +
104B THR* 4.0 3.4 - - - -
196C GLY* 3.5 23.9 - - - +
212C ILE* 4.1 2.0 - - + -
213C VAL 4.0 4.9 - - - +
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA* 1.3 72.7 - - - +
57B HIS* 1.3 62.9 + - - +
58B CYS 3.0 1.8 + - - -
59B GLY* 3.3 12.5 + - - -
90B LYS* 4.1 11.9 - - + +
94B TYR* 3.6 38.3 - - + -
102B ASP* 2.8 15.4 + - - +
103B ILE 3.6 20.6 - - - +
104B THR* 3.3 15.8 + - - +
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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