Contacts of the helix formed by residues 80 - 92 (chain A) in PDB entry 1G9Y
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 GLU 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A VAL* 2.9 29.7 - - - +
65A GLY* 4.1 6.8 + - - -
78A LEU* 4.4 3.6 - - + +
79A SER* 1.3 73.0 - - - +
81A ILE* 1.3 66.7 + - - +
82A LYS 3.4 1.1 - - - -
83A PRO* 3.0 19.2 - - + +
84A LEU* 2.9 22.7 + - - +
404C A 3.3 45.9 + - - +
405C A 4.0 14.0 + - - +
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Residues in contact with ILE 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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39A LEU 5.9 2.7 - - - +
41A LEU* 5.0 12.3 - - + -
79A SER 2.8 13.4 + - - +
80A GLU* 1.3 69.6 - - - +
82A LYS* 1.3 59.2 + - + +
84A LEU* 3.5 6.2 + - - +
85A HIS* 3.0 27.2 + - - +
109A ILE* 3.4 36.3 - - + +
112A LEU* 3.4 28.7 - - + -
403C A 4.3 26.0 - - + +
404C A 2.8 20.0 + - - +
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Residues in contact with LYS 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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2A ASN* 5.9 3.4 - - - -
81A ILE* 1.3 74.2 - - - +
83A PRO* 1.3 77.7 - - + +
85A HIS* 3.1 18.3 + - + +
86A ASN* 3.0 22.9 + - + +
109A ILE* 6.5 0.4 - - + -
404C A 4.8 1.6 + - - +
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Residues in contact with PRO 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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5A TYR* 5.3 1.0 + - - -
64A VAL* 3.8 36.1 - - + +
78A LEU* 4.4 3.5 - - + +
80A GLU* 3.0 38.6 - - + +
82A LYS* 1.3 90.9 - - + +
84A LEU* 1.3 55.0 + - - +
86A ASN* 3.7 8.8 + - + +
87A PHE* 2.9 32.2 + - - +
404C A 5.2 1.6 - - - +
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Residues in contact with LEU 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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41A LEU* 3.9 30.7 - - + +
42A THR 4.7 2.2 - - - +
43A PHE* 3.6 31.4 - - + +
78A LEU* 4.1 25.5 - - + +
79A SER 4.2 11.7 - - - +
80A GLU 2.9 18.4 + - - +
81A ILE* 3.5 4.9 - - - +
83A PRO* 1.3 74.6 - - - +
85A HIS* 1.3 61.5 + - - +
87A PHE* 4.9 0.2 - - + -
88A LEU* 2.9 59.4 + - + +
105A VAL* 4.2 6.5 - - + -
109A ILE* 4.2 12.6 - - + -
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Residues in contact with HIS 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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81A ILE 3.0 14.3 + - - +
82A LYS* 3.1 20.4 + - + +
84A LEU* 1.3 79.1 - - - +
86A ASN* 1.3 60.9 + - - +
89A THR* 2.7 51.8 + - + -
106A LEU* 3.6 22.3 - - + +
109A ILE* 3.8 30.0 - - + +
110A GLU* 3.2 33.0 + - + +
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Residues in contact with ASN 86 (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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2A ASN* 3.4 30.0 + - - +
3A THR* 2.9 39.6 + - - +
5A TYR* 3.8 8.7 + - - -
82A LYS* 3.0 13.5 + - + +
83A PRO* 3.7 11.4 + - + +
85A HIS* 1.3 80.8 + - - +
87A PHE* 1.3 62.0 + - - +
89A THR* 3.6 4.5 - - - -
90A GLN* 3.1 43.8 + - - +
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Residues in contact with PHE 87 (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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5A TYR* 3.9 33.0 - + + +
9A PHE* 4.8 2.0 - + - -
10A LEU* 4.6 8.7 - - + -
13A LEU* 3.5 33.0 - - + -
43A PHE* 3.5 37.5 - + - -
62A ILE* 3.9 17.0 - - + -
78A LEU* 4.1 21.8 - - + -
83A PRO 2.9 17.5 + - - +
84A LEU 3.9 1.6 - - - +
86A ASN* 1.3 76.9 - - - +
88A LEU* 1.3 71.0 + - + +
90A GLN* 3.1 4.5 + - - +
91A LEU* 2.9 48.2 + - + +
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Residues in contact with LEU 88 (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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23A ILE* 4.2 25.1 - - + -
43A PHE* 4.2 7.9 - - + -
84A LEU* 2.9 44.4 + - + +
87A PHE* 1.3 84.2 - - + +
89A THR* 1.3 60.4 + - - +
91A LEU* 4.2 14.6 - - + -
92A GLN* 2.8 36.2 + - - +
102A ALA* 4.4 11.9 - - + +
105A VAL* 3.6 34.1 - - + -
106A LEU* 3.7 19.1 - - + -
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Residues in contact with THR 89 (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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85A HIS* 2.7 43.9 + - + -
86A ASN* 3.6 7.6 - - - +
87A PHE 3.2 0.2 - - - -
88A LEU* 1.3 77.9 - - - +
90A GLN* 1.3 67.5 + - + +
92A GLN* 4.0 6.5 - - - +
93A PRO* 3.5 13.9 - - - +
106A LEU* 3.8 11.5 - - - +
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Residues in contact with GLN 90 (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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3A THR 3.1 23.6 + - - -
4A LYS* 3.7 5.0 - - - +
5A TYR* 2.9 41.2 + - + +
10A LEU* 3.6 29.2 - - + +
86A ASN* 3.1 27.4 + - - +
87A PHE 3.1 6.7 + - - +
89A THR* 1.3 83.7 - - + +
91A LEU* 1.3 64.0 + - - +
93A PRO* 3.2 15.7 - - - +
94A PHE* 3.8 3.5 - - - -
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Residues in contact with LEU 91 (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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10A LEU* 3.6 34.0 - - + +
13A LEU* 4.2 11.0 - - + -
14A ALA* 3.6 18.8 - - + +
17A VAL* 4.4 5.8 - - + -
23A ILE* 5.5 0.2 - - + -
43A PHE* 4.1 13.9 - - + -
87A PHE* 2.9 46.1 + - + +
88A LEU* 4.1 12.3 - - + +
90A GLN* 1.3 77.3 - - - +
92A GLN* 1.3 66.2 + - - +
93A PRO* 3.4 0.2 - - - +
94A PHE* 3.0 22.9 + - - +
95A LEU* 3.7 24.6 + - + -
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Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU 2.8 23.5 + - - +
89A THR* 4.0 7.3 - - - +
91A LEU* 1.3 72.4 - - - +
93A PRO* 1.3 77.5 - - + +
94A PHE 3.1 1.2 + - - -
95A LEU* 3.2 20.8 + - - +
99A GLN* 2.8 57.9 + - + +
102A ALA* 4.4 9.2 - - + -
103A ASN* 2.9 37.6 + - - +
106A LEU* 4.7 1.8 - - + -
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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