Contacts of the helix formed by residues 96 - 104 (chain A) in PDB entry 1T43
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A TRP* 4.1 24.7 + - - +
93A PRO 3.5 10.1 - - - +
94A ASP* 2.8 10.8 + - - +
95A THR* 1.3 74.3 - - - +
97A CYS* 1.3 74.4 + - + +
98A LEU 3.2 0.7 - - - -
99A VAL* 3.2 3.0 + - - +
100A GLU* 2.7 63.2 + - - +
262A ARG 4.6 1.0 - - - +
263A ASP* 3.0 31.2 - - + +
264A TYR* 4.2 16.4 - - + +
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Residues in contact with CYS 97 (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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94A ASP 4.5 2.7 - - - +
96A GLU* 1.3 84.3 - - - +
98A LEU* 1.3 57.7 + - - +
100A GLU* 4.5 1.1 - - - -
101A GLN* 2.5 55.3 + - - +
261A CYS* 3.6 20.6 - - - -
262A ARG 2.2 40.4 - - - -
263A ASP* 3.7 11.2 - - + -
270A VAL* 3.0 22.0 - - + -
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 3.8 16.5 - - + +
96A GLU 3.2 1.4 - - - +
97A CYS* 1.3 79.8 - - - +
99A VAL* 1.3 57.5 + - - +
101A GLN* 4.6 0.7 - - - +
102A ALA* 3.0 28.8 + - - +
123A ILE* 3.2 30.3 - - + -
181A VAL* 3.2 29.8 - - + -
182A SER 3.8 22.2 - - - +
183A ASN* 4.0 8.3 - - + -
235A LEU* 3.7 26.0 - - + +
236A LEU 4.4 0.2 - - - +
237A GLU* 4.1 9.0 - - + +
270A VAL* 3.5 18.2 - - + +
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Residues in contact with VAL 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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77A PHE* 3.9 13.5 - - + -
78A TRP* 6.1 3.4 - - + -
95A THR* 3.4 18.8 - - + +
96A GLU* 3.2 6.0 + - - +
98A LEU* 1.3 75.6 - - - +
100A GLU* 1.3 64.9 + - + +
102A ALA* 3.7 4.5 - - - +
103A LEU* 3.3 36.8 + - + +
123A ILE* 3.8 31.9 - - + -
126A ALA* 4.3 20.2 - - + +
127A LEU* 4.4 12.8 - - + -
130A GLU* 6.1 0.4 - - - +
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Residues in contact with GLU 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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78A TRP* 4.9 7.3 + - + +
96A GLU* 2.7 63.5 + - + +
97A CYS* 3.8 2.2 - - - +
99A VAL* 1.3 71.3 - - + +
101A GLN* 1.3 72.4 + - - +
103A LEU* 3.5 6.6 + - - +
104A ALA* 2.8 27.4 + - - +
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Residues in contact with GLN 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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97A CYS* 2.5 60.7 + - - +
98A LEU* 4.6 1.3 - - + +
100A GLU* 1.3 82.4 + - - +
102A ALA* 1.3 68.1 + - - +
104A ALA* 3.1 10.7 + - + +
105A ARG* 3.0 41.1 + - - +
235A LEU* 4.6 3.6 - - + -
261A CYS* 4.4 23.7 - - + +
270A VAL* 5.6 2.7 - - + -
272A LEU* 5.0 9.9 - - + -
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Residues in contact with ALA 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 LEU 3.0 21.8 + - - +
99A VAL* 3.7 6.3 - - - +
101A GLN* 1.3 78.7 - - - +
103A LEU* 1.3 56.6 + - - +
105A ARG 3.1 3.3 + - - -
106A LEU* 2.8 30.8 + - - +
123A ILE* 5.8 0.2 - - + -
127A LEU* 4.1 20.0 - - + -
179A MET* 3.2 13.5 - - + +
181A VAL* 4.9 7.0 - - + -
235A LEU* 3.6 23.3 - - + +
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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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99A VAL* 3.3 30.2 + - + +
100A GLU* 3.7 5.6 - - - +
102A ALA* 1.3 76.0 - - - +
104A ALA* 1.3 51.9 + - - +
105A ARG 2.6 6.4 + - - -
106A LEU* 3.4 23.3 - - + -
107A PRO* 2.4 40.7 - - - +
126A ALA 5.2 1.8 - - - +
127A LEU* 4.5 10.5 - - + +
130A GLU* 4.4 31.6 - - + +
131A ARG* 4.3 17.9 - - + +
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Residues in contact with ALA 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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100A GLU 2.8 21.6 + - - +
101A GLN* 3.1 17.0 + - + +
103A LEU* 1.3 70.3 - - - +
105A ARG* 1.3 62.4 + - + +
107A PRO* 3.9 6.9 - - - +
108A GLU* 3.1 13.5 - - - +
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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