Contacts of the strand formed by residues 34 - 37 (chain Q) in PDB entry 1G3I
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 VAL 34 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q ILE* 4.6 1.6 - - + -
14Q VAL* 3.3 47.8 - - + +
15Q GLY 3.8 3.1 - - - -
16Q GLY* 3.7 17.3 - - - +
32Q ARG* 4.6 6.6 - - - +
33Q LYS* 1.3 84.3 - - - +
35Q ARG* 1.3 70.3 + - - +
43Q LEU* 5.1 0.7 - - + -
44Q ALA 3.1 16.6 - - - +
45Q GLY* 4.3 3.6 - - - -
168Q THR* 3.7 25.5 + - - +
170Q GLU* 4.1 25.3 - - + +
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Residues in contact with ARG 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q ARG* 3.3 60.7 + - - +
33Q LYS 4.2 0.2 - - - -
34Q VAL* 1.3 81.7 - - - +
36Q ARG* 1.3 65.3 + - - +
43Q LEU* 4.0 2.8 - - - +
44Q ALA* 2.8 32.3 + - - +
46Q PHE* 4.1 10.1 - - + -
54Q PHE* 4.0 24.3 - - - -
57Q PHE* 3.5 32.7 - - + -
170Q GLU* 5.2 1.1 - - - -
440X SER 4.3 9.4 - - - -
441X ARG* 3.0 31.4 + - - +
442X PHE* 5.0 0.4 - - - +
443X ILE 3.3 19.8 + - - -
444X LEU* 4.4 6.5 + - - +
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Residues in contact with ARG 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q ARG* 1.3 79.0 - - - +
37Q LEU* 1.3 70.3 + - - +
39Q ASN 5.8 0.2 - - - -
40Q GLY* 4.3 25.5 + - - +
42Q VAL 3.8 4.7 + - - +
43Q LEU* 3.6 14.3 - - + +
170Q GLU* 3.5 34.4 + - + +
171Q GLU 3.0 25.2 + - - +
172Q LEU* 3.5 24.4 - - - +
173Q PRO 4.9 5.1 + - - -
441X ARG* 4.0 15.8 + - - -
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Residues in contact with LEU 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q ARG 4.2 0.4 + - - -
36Q ARG* 1.3 79.1 - - - +
38Q TYR* 1.3 74.0 + - - +
39Q ASN 3.5 1.8 - - - +
40Q GLY 3.4 0.8 + - - -
41Q LYS 3.1 3.1 + - - -
42Q VAL* 2.9 42.2 + - + +
44Q ALA* 4.8 5.1 - - + +
57Q PHE* 3.8 38.4 - - + +
60Q PHE* 4.3 9.2 - - + -
61Q GLU* 3.1 61.2 - - + +
64Q LEU* 4.0 14.8 - - + -
441X ARG* 4.2 7.0 - - - +
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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
------------------------------------------------------------
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