Contacts of the helix formed by residues 97 - 107 (chain A) in PDB entry 1ATT
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A CYS* 4.5 1.4 - - - +
24A TYR* 5.8 0.5 - - - +
96A CYS* 1.3 88.6 - - - +
98A ASN* 1.3 65.1 + - + +
100A LEU* 3.8 4.8 - - - +
101A THR* 3.2 21.7 + - - -
351A ARG* 2.3 42.2 + - - +
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Residues in contact with ASN 98 (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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96A CYS 3.1 0.2 + - - -
97A ASN* 1.3 78.6 - - + +
99A THR* 1.3 62.1 + - - +
100A LEU 3.0 2.0 - - - -
101A THR* 3.1 16.9 + - - +
102A GLN* 2.9 53.0 + - - +
343A ASP* 3.5 19.2 - - - +
351A ARG* 5.2 2.3 - - + +
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Residues in contact with THR 99 (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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95A ALA* 3.9 5.2 - - + -
96A CYS 3.3 10.1 - - - -
98A ASN* 1.3 78.9 - - - +
100A LEU* 1.3 57.4 + - - +
102A GLN* 3.6 3.3 + - - +
103A LEU* 3.0 34.7 + - + +
341A LEU* 4.7 1.0 - - - +
343A ASP* 4.1 11.2 + - - +
344A LEU* 3.6 26.5 - - + +
349A LYS 3.8 8.0 + - - -
350A SER* 3.9 1.6 - - - -
351A ARG* 2.9 29.2 + - - +
352A LEU* 3.4 31.9 - - + -
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Residues in contact with LEU 100 (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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22A CYS* 3.9 33.9 - - + +
23A ILE 4.2 7.9 - - - +
24A TYR* 4.1 4.7 - - + +
92A LYS* 3.8 18.6 - - + +
95A ALA* 4.1 26.7 - - + +
96A CYS* 3.6 9.7 + - - -
97A ASN 3.8 10.1 - - - +
99A THR* 1.3 77.6 - - - +
101A THR* 1.4 66.3 + - - +
102A GLN 2.9 1.0 + - - -
103A LEU* 2.9 4.1 + - - +
104A MET* 2.9 52.2 + - + +
117A SER* 4.0 17.3 - - - +
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Residues in contact with THR 101 (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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24A TYR* 3.9 43.7 - - + +
97A ASN 3.2 14.4 + - - -
98A ASN* 3.1 23.4 + - - +
100A LEU* 1.4 75.2 - - - +
102A GLN* 1.3 58.6 + - + +
104A MET* 3.5 2.8 + - - +
105A GLU* 2.9 41.8 + - + +
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Residues in contact with GLN 102 (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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98A ASN* 2.9 37.6 + - - +
99A THR* 3.9 4.9 - - - +
100A LEU 2.9 0.6 + - - -
101A THR* 1.3 76.3 - - + +
103A LEU* 1.3 59.5 + - - +
105A GLU* 3.7 11.4 - - + +
106A VAL* 2.8 35.7 + - + +
340A GLY 3.7 15.9 - - - +
341A LEU* 3.8 12.3 - - + -
342A GLU* 2.8 30.3 + - - +
343A ASP* 2.8 31.7 + - - +
344A LEU 4.4 1.0 + - - -
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Residues in contact with LEU 103 (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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88A PHE* 4.2 25.8 - - + +
91A THR* 4.8 2.0 - - + -
92A LYS* 3.7 28.9 - - + +
95A ALA* 3.8 24.9 - - + -
99A THR* 3.0 29.3 + - + +
100A LEU 2.9 7.5 + - - +
102A GLN* 1.3 72.5 - - - +
104A MET* 1.3 63.1 + - - +
107A PHE* 3.3 54.1 + - + +
109A PHE* 4.1 1.8 - - + -
341A LEU* 3.7 17.3 - - + -
344A LEU* 4.2 12.3 - - + -
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Residues in contact with MET 104 (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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24A TYR* 3.5 34.8 - - + -
25A ARG* 6.1 1.6 - - + -
92A LYS* 3.4 33.2 - - - -
100A LEU* 2.9 29.2 + - + +
101A THR 3.7 4.5 - - - +
103A LEU* 1.3 75.6 - - - +
105A GLU* 1.3 62.6 + - - +
109A PHE* 3.0 53.3 + - + +
110A ASP* 3.2 12.2 + - + +
116A THR 5.4 0.2 - - - -
117A SER* 3.8 22.4 - - - +
120A ILE* 3.9 14.6 - - + -
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Residues in contact with GLU 105 (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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24A TYR* 6.0 1.6 - - + +
101A THR* 2.9 31.0 + - + +
102A GLN* 3.0 12.0 + - - +
104A MET* 1.3 78.1 - - - +
106A VAL* 1.3 67.9 + - + +
108A LYS* 3.2 15.6 + - - +
110A ASP* 3.7 16.7 - - + +
339A MET 5.7 0.9 - - - +
340A GLY* 5.8 2.3 - - - -
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Residues in contact with VAL 106 (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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59A PHE* 3.6 13.0 - - + -
62A ALA* 5.9 1.2 - - - +
102A GLN* 2.8 21.2 + - + +
105A GLU* 1.3 75.8 - - + +
107A PHE* 1.3 69.8 + - + +
108A LYS* 3.0 15.6 + - - +
336A LEU* 3.9 27.4 - - + -
339A MET* 3.5 35.0 - - + +
340A GLY* 3.8 4.0 - - - -
341A LEU* 3.5 34.8 - - + +
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Residues in contact with PHE 107 (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 ALA 4.4 4.5 - - - +
56A ASN* 4.9 1.9 + - - -
59A PHE* 3.3 52.4 - + + +
84A ILE* 4.1 9.4 - - + -
85A SER* 4.4 10.5 - - - +
88A PHE* 3.3 47.1 - + + -
103A LEU* 3.3 38.9 + - + +
106A VAL* 1.3 78.3 - - + +
108A LYS* 1.3 64.4 + - - +
109A PHE* 2.9 35.7 + + + -
336A LEU* 3.9 15.0 - - + -
341A LEU* 3.9 9.2 - - + -
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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