Contacts of the helix formed by residues 98 - 108 (chain A) in PDB entry 1TJY
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A VAL* 4.8 3.8 - - + -
73A GLN* 3.5 43.1 - - + +
74A VAL* 4.1 15.9 - - + +
77A VAL* 4.8 7.9 - - + -
90A VAL* 3.9 22.2 - - + -
92A ALA* 4.1 10.3 - - + -
93A VAL* 4.4 11.0 - - + -
94A SER* 4.2 17.0 + - - +
95A PRO 5.4 0.2 - - - -
96A ASP 3.3 1.0 - - - -
97A GLY* 1.3 83.2 - - - +
99A CYS* 1.3 65.6 + - - +
100A PRO* 3.5 1.6 - - - -
101A ALA* 3.2 6.9 + - + +
102A LEU* 3.0 42.9 + - + +
119A THR* 4.7 4.5 - - + -
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Residues in contact with CYS 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 PRO 3.6 22.4 - - - -
96A ASP* 3.1 16.5 + - - +
98A LEU* 1.3 77.6 - - - +
100A PRO* 1.3 71.1 - - + +
102A LEU* 4.5 0.7 - - - +
103A LYS* 2.8 37.3 + - + +
119A THR* 4.7 1.8 - - - -
120A LYS* 4.0 8.7 - - - +
123A CYS* 2.0 50.3 - - - -
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Residues in contact with PRO 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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96A ASP 3.9 7.0 - - - +
97A GLY* 4.0 8.1 - - - +
98A LEU 3.7 2.5 - - - -
99A CYS* 1.3 93.5 - - + +
101A ALA* 1.3 60.4 + - - +
103A LYS* 3.9 6.1 - - + +
104A ARG* 3.1 23.6 + - - +
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Residues in contact with ALA 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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74A VAL* 4.1 17.7 - - + -
77A VAL* 3.8 21.3 - - + +
78A ASN* 3.6 33.9 + - - +
81A VAL* 4.8 1.0 - - - +
98A LEU* 3.2 9.9 + - - +
100A PRO* 1.3 78.9 - - - +
102A LEU* 1.3 58.1 + - - +
104A ARG* 3.4 5.7 + - - +
105A ALA* 3.0 25.8 + - - +
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Residues in contact with LEU 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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77A VAL* 3.8 29.2 - - + -
88A ILE* 5.2 1.3 - - + -
90A VAL* 4.4 11.9 - - + -
98A LEU* 3.0 41.0 + - + +
99A CYS* 3.9 2.9 - - - +
101A ALA* 1.3 74.1 - - - +
103A LYS* 1.3 61.3 + - - +
105A ALA* 3.3 5.6 + - - +
106A MET* 3.0 33.2 + - - +
112A ILE* 3.8 30.0 - - + +
114A THR* 5.4 0.4 - - + -
119A THR* 3.8 21.5 - - + +
123A CYS* 3.4 25.8 - - + +
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Residues in contact with LYS 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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99A CYS* 2.8 24.8 + - + +
100A PRO* 3.9 6.1 - - + +
102A LEU* 1.3 74.3 - - - +
104A ARG* 1.3 58.6 + - - +
106A MET* 3.3 18.6 + - + +
107A GLN* 2.9 46.7 + - - +
120A LYS* 5.5 4.6 - - - +
122A GLU* 4.1 25.0 + - - +
123A CYS* 3.9 23.7 - - - -
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Residues in contact with ARG 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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78A ASN* 3.7 26.7 - - - +
81A VAL* 3.6 16.2 - - - +
82A ASN* 2.9 37.7 + - - +
100A PRO 3.1 17.9 + - - +
101A ALA* 3.5 5.6 - - - +
102A LEU 3.3 0.2 - - - -
103A LYS* 1.3 74.1 - - - +
105A ALA* 1.3 63.7 + - - +
107A GLN* 3.3 18.6 + - - +
108A ARG* 3.2 62.4 + - - +
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Residues in contact with ALA 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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77A VAL* 4.8 1.6 - - + -
81A VAL* 3.4 34.0 - - + +
101A ALA 3.0 12.2 + - - +
102A LEU* 3.4 10.1 - - - +
104A ARG* 1.3 77.1 - - - +
106A MET* 1.3 60.4 + - - +
108A ARG* 3.1 9.9 + - - +
110A VAL* 3.0 28.1 + - + +
112A ILE* 3.6 25.1 - - + -
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Residues in contact with MET 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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102A LEU 3.0 19.6 + - - +
103A LYS* 3.8 13.9 - - + +
105A ALA* 1.3 72.7 - - - +
107A GLN* 1.3 66.7 + - - +
109A GLY* 3.0 13.3 + - - -
110A VAL 3.8 9.4 - - - +
112A ILE* 3.6 18.8 - - + +
122A GLU 3.6 14.8 - - - +
123A CYS* 3.5 29.6 - - - +
124A ARG* 4.0 24.5 - - - +
125A SER* 4.1 11.7 - - - +
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Residues in contact with GLN 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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103A LYS* 2.9 32.8 + - - +
104A ARG* 3.5 18.1 - - - +
105A ALA 3.3 0.2 - - - -
106A MET* 1.3 76.7 - - - +
108A ARG* 1.3 61.9 + - + +
109A GLY 3.4 0.7 + - - -
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Residues in contact with ARG 108 (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 VAL* 3.9 18.8 + - - +
82A ASN* 3.7 14.8 - - - +
104A ARG* 3.2 54.8 + - + +
105A ALA* 3.1 9.1 + - - +
106A MET 3.1 1.0 - - - -
107A GLN* 1.3 79.3 - - + +
109A GLY* 1.3 60.1 + - - +
110A VAL* 3.3 10.8 + - + +
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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