Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 2G9Y
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 LEU 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.3 22.7 - - + -
36A SER* 3.4 30.1 - - - +
37A LEU* 4.0 17.5 - - + -
79A PRO* 1.3 81.6 - - + +
81A THR* 1.3 62.2 + - - +
420A ALA* 3.3 3.3 - - - +
421A ALA 2.8 36.5 + - - +
422A TYR* 5.7 0.4 - - - -
426A ALA* 3.4 39.9 - - + +
427A ALA 3.7 4.9 - - - +
429A VAL* 3.5 5.2 - - - +
430A VAL* 3.9 21.3 - - + -
33B LEU* 4.7 3.1 - - + -
80B LEU* 6.4 1.8 - - + -
430B VAL* 4.9 3.4 - - + -
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU 3.8 10.3 - - - +
79A PRO 3.8 1.2 + - - -
80A LEU* 1.3 79.0 - - - +
82A GLY* 1.3 59.1 + - - +
418A ARG* 3.7 15.9 - - - +
419A ILE 3.5 6.3 - - - -
420A ALA* 3.6 20.2 - - + -
429A VAL* 3.9 4.7 - - - -
430A VAL* 3.5 14.1 - - - +
81B THR* 2.8 38.7 + - - +
82B GLY* 3.4 5.7 - - - -
83B GLN* 3.7 13.9 - - - +
430B VAL* 4.2 2.6 - - - +
431B GLY* 3.1 22.8 + - - -
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Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A THR* 1.3 75.3 - - - +
83A GLN* 1.3 64.8 + - - -
418A ARG* 3.4 1.0 - - - -
419A ILE* 2.9 29.5 + - - -
429A VAL 3.2 15.7 + - - -
431A GLY 3.5 3.8 - - - -
81B THR* 3.4 12.8 - - - -
83B GLN* 3.2 14.4 + - - -
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Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASP* 5.6 0.4 - - - +
82A GLY* 1.3 77.7 + - - +
84A TYR* 1.3 62.2 + - - +
416A GLN* 3.9 21.1 - - + +
417A LEU 3.2 13.2 - - - +
418A ARG 4.9 0.2 - - - +
419A ILE* 4.1 2.0 - - - +
431A GLY 3.2 10.0 + - - +
432A LEU* 3.4 8.9 - - + +
433A THR* 3.2 20.6 + - - -
55B ASP* 3.2 23.6 - - - +
81B THR* 3.7 14.3 + - - +
82B GLY 3.3 15.6 + - - -
83B GLN* 2.8 32.3 - - + +
418B ARG* 3.4 32.7 + - - +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLN* 1.3 73.1 - - - +
85A THR* 1.3 63.8 + - - +
86A HIS* 4.0 6.6 - + - -
109A TRP* 4.4 5.4 - - - -
367A THR* 3.5 26.3 - - + +
368A ALA 2.6 26.2 + - - -
369A ASP* 4.3 0.2 - - - -
416A GLN* 3.5 4.7 - - - -
417A LEU* 2.9 41.9 + - + -
419A ILE* 3.9 30.2 - - + +
432A LEU* 4.8 0.4 - - - -
433A THR* 3.1 28.0 - - - +
434A ASP 3.9 4.5 - - - -
435A GLN* 3.1 50.4 + - + +
438A LEU* 4.3 11.2 - - + +
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TYR* 1.3 75.2 - - - +
86A HIS* 1.3 61.7 + - - +
87A TYR* 3.8 11.7 - - + -
414A GLY 6.1 0.2 - - - -
416A GLN* 4.3 10.3 - - + +
432A LEU* 4.3 8.5 - - + -
433A THR 3.1 4.3 + - - -
434A ASP* 2.9 25.8 + - - +
435A GLN* 2.9 27.2 + - - +
24B ARG* 3.1 32.5 + - - +
59B THR* 5.2 6.3 - - + -
62B ARG* 3.6 24.5 - - - +
63B ASN* 6.1 0.9 - - - +
68B ALA 4.8 2.0 - - - +
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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