Contacts of the strand formed by residues 34 - 38 (chain D) in PDB entry 5GJQ
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 CYS 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D GLY 4.1 4.9 - - - +
33D THR* 1.3 78.2 - - - +
35D LEU* 1.3 62.3 + - - +
45D LEU* 4.9 1.3 - - - -
46D ALA 3.6 7.4 - - - -
47D ALA* 3.9 12.3 - - + -
64D LYS* 4.3 4.9 - - - +
75D SER* 3.0 39.0 - - - +
76D VAL 4.5 7.4 - - - +
135D LEU* 3.6 17.8 - - - +
163D CYS* 3.4 1.5 - - - -
164D ILE* 2.6 52.4 + - + +
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Residues in contact with LEU 35 (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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33D THR* 5.3 0.7 - - + -
34D CYS* 1.3 75.9 - - - +
36D GLY* 1.3 70.5 + - - +
37D ILE* 4.7 7.4 - - + +
44D LEU* 5.4 1.3 - - + -
45D LEU* 3.4 5.0 - - - +
46D ALA* 2.9 39.5 + - + +
135D LEU* 3.9 6.3 - - - -
162D THR 3.4 14.1 - - - +
163D CYS* 3.8 16.2 - - + +
175D LEU* 5.2 11.4 - - + -
193D ALA* 4.4 22.9 - - + +
196D VAL* 4.1 26.9 - - + -
197D LEU* 3.6 37.7 - - + +
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Residues in contact with GLY 36 (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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35D LEU* 1.3 79.3 - - - +
37D ILE* 1.3 61.7 + - - +
44D LEU 3.1 12.1 - - - -
45D LEU* 4.2 10.3 - - - -
135D LEU* 4.0 4.3 - - - +
147D LEU* 3.4 14.6 - - - +
161D ALA* 3.2 3.1 - - - +
162D THR 2.9 33.9 + - - +
175D LEU* 4.9 0.7 - - - +
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Residues in contact with ILE 37 (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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35D LEU* 4.7 8.9 - - + +
36D GLY* 1.3 75.2 - - - +
38D LEU* 1.3 63.4 + - - +
43D VAL* 3.4 4.6 - - - +
44D LEU* 3.0 50.5 + - + +
147D LEU* 4.8 0.4 - - - -
160D LYS 4.1 2.9 - - - -
161D ALA* 4.1 8.3 - - + -
175D LEU* 5.6 3.4 - - + -
179D TYR* 4.9 4.7 - - + -
180D LYS* 6.4 0.2 - - - -
189D ALA* 4.3 16.3 - - + +
192D LEU* 5.4 9.0 - - + -
193D ALA* 6.0 0.4 - - + +
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Residues in contact with LEU 38 (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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36D GLY 4.3 0.2 - - - -
37D ILE* 1.3 76.2 - - - +
39D ALA* 1.3 72.8 + - - +
43D VAL* 4.0 15.9 - - + -
145D PHE* 3.6 44.9 - - + +
146D GLN* 4.1 10.3 - - - +
147D LEU* 4.7 3.3 - - + +
159D TRP 4.5 6.1 - - - +
160D LYS* 2.8 47.9 + - + +
179D TYR* 2.6 27.3 + - - +
184D MET* 3.7 4.2 - - - +
189D ALA* 5.0 3.0 - - - +
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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