Contacts of the helix formed by residues 93 - 105 (chain B) in PDB entry 1T9A
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 THR 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLY 5.5 0.4 - - - +
92B LEU* 1.3 76.0 - - - +
94B GLY* 1.3 66.1 + - - +
95B GLY* 3.4 4.2 + - - -
96B GLN* 2.8 45.2 + - - +
97B ILE* 2.9 22.6 + - - +
120B PRO 4.9 1.9 + - - -
124B ALA* 4.7 1.6 - - - +
254B THR 3.7 8.9 + - - -
255B ALA* 4.1 9.2 - - - +
256B ALA 3.1 9.0 - - - -
257B ILE* 3.9 21.3 - - + -
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Residues in contact with GLY 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B THR* 1.3 71.9 - - - +
95B GLY* 1.3 57.0 + - - +
97B ILE* 3.3 1.8 + - - -
98B PHE* 2.9 25.2 + - - +
223B VAL* 3.8 14.1 - - - +
226B LEU* 3.1 28.4 - - - +
253B VAL 3.9 0.9 - - - -
254B THR* 3.1 19.2 + - - -
256B ALA 2.9 12.9 + - - -
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Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 3.0 2.6 + - - -
94B GLY* 1.3 77.6 - - - +
96B GLN* 1.3 61.4 + - - +
98B PHE* 3.1 10.5 + - - +
99B ASN* 3.0 17.5 + - - +
120B PRO 3.9 9.4 - - - -
121B VAL* 4.0 14.7 - - - +
124B ALA* 3.1 21.7 - - - +
125B ILE* 4.9 0.3 - - - +
254B THR* 2.8 15.1 + - - +
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Residues in contact with GLN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLY 4.3 1.9 - - - +
92B LEU* 3.4 32.3 - - + +
93B THR* 2.8 45.3 + - + +
95B GLY* 1.3 73.0 - - - +
97B ILE* 1.3 66.5 + - - +
99B ASN* 3.0 7.8 + - - +
100B GLU* 3.0 24.9 + - - +
124B ALA* 3.7 17.3 - - + +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 4.0 32.8 - - + +
92B LEU* 4.0 16.2 - - + +
93B THR 2.9 13.2 + - - +
94B GLY 3.5 7.4 - - - +
96B GLN* 1.3 77.0 - - - +
98B PHE* 1.3 57.7 + - - +
100B GLU* 3.2 7.7 + - - +
101B MET* 2.8 36.5 + - + +
223B VAL* 3.6 33.4 - - + +
226B LEU* 4.1 11.2 - - + -
227B PRO* 3.8 25.8 - - + -
258B LEU* 4.2 15.5 - - + -
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Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLY 2.9 13.3 + - - +
95B GLY* 3.1 13.2 - - - +
97B ILE* 1.3 77.2 - - - +
99B ASN* 1.3 63.7 + - - +
101B MET* 3.3 2.9 + - - +
102B MET* 3.1 57.6 + - + +
110B VAL* 5.5 2.7 - - + -
121B VAL* 3.5 23.6 - - + -
125B ILE* 4.2 11.9 - - + -
131B PHE* 5.1 3.1 - + - -
158B VAL* 5.0 3.1 - - + -
160B LEU* 4.1 21.8 - - + -
187B PHE* 3.6 47.1 - + + -
226B LEU* 4.8 3.4 - - + -
230B ILE* 4.1 22.7 - - + -
249B LEU* 4.5 10.8 - - + -
254B THR* 6.2 0.4 - - + -
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLY 3.0 11.8 + - - +
96B GLN* 3.0 11.6 + - - +
98B PHE* 1.3 84.2 - - - +
100B GLU* 1.3 65.6 + - + +
102B MET* 3.3 10.8 + - - +
103B SER 3.6 6.4 + - - -
124B ALA 3.5 22.2 - - - +
125B ILE* 3.7 6.1 - - + +
128B SER* 2.9 29.5 + - - -
130B LYS* 3.6 20.3 - - - +
131B PHE* 3.2 24.5 - - - -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 3.7 29.6 - - + -
92B LEU* 4.3 13.5 - - + +
96B GLN* 3.0 15.2 + - + +
97B ILE 3.5 7.2 - - - +
99B ASN* 1.3 80.4 - - - +
101B MET* 1.3 60.0 + - - +
103B SER* 3.0 17.7 + - - -
104B ARG* 2.9 25.3 + - + +
130B LYS* 3.5 31.6 + - - +
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Residues in contact with MET 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 3.8 26.5 - - - -
97B ILE* 2.8 30.9 + - + +
98B PHE 3.7 4.7 - - - +
100B GLU* 1.3 70.1 - - - +
102B MET* 1.3 62.0 - - + +
104B ARG* 3.2 15.2 + - + +
105B GLN* 2.9 34.0 + - - +
227B PRO* 4.0 13.5 - - + +
230B ILE* 3.8 35.0 - - + -
231B ASN* 3.2 38.8 - - - +
267B THR 3.7 11.9 - - - +
269B PRO* 5.3 0.2 - - + -
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Residues in contact with MET 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PHE* 3.1 60.9 + - + +
99B ASN 3.6 6.7 - - - +
100B GLU 3.2 0.4 - - - -
101B MET* 1.3 80.6 - - + +
103B SER* 1.3 60.5 + - - +
105B GLN 3.4 0.7 + - - -
106B ASN 3.2 3.6 + - - -
107B VAL* 2.8 51.4 + - + +
110B VAL* 4.7 2.0 - - + -
131B PHE* 3.7 29.2 - - + -
158B VAL* 4.2 15.7 - - - -
187B PHE* 4.1 5.8 - - + -
230B ILE* 4.2 7.6 - - + -
234B PHE* 4.0 22.0 - - + -
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Residues in contact with SER 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASN 3.6 1.6 + - - -
100B GLU* 3.0 14.0 + - - -
102B MET* 1.3 76.2 - - - +
104B ARG* 1.3 61.3 + - - +
106B ASN* 2.8 25.0 + - - +
107B VAL 4.8 3.8 - - - +
130B LYS* 3.7 42.0 + - - +
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Residues in contact with ARG 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ASP* 4.4 3.6 + - - -
88B SER* 4.4 8.9 + - - -
89B PHE* 3.4 28.0 - - - -
100B GLU* 2.9 24.4 + - - +
101B MET* 3.2 22.4 + - + +
103B SER* 1.3 74.7 - - - +
105B GLN* 1.3 54.1 + - - +
106B ASN* 2.6 20.4 - - - +
267B THR* 2.7 49.9 + - - -
268B LEU* 3.6 17.7 - - - +
269B PRO* 3.7 25.6 - - + +
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B MET* 2.9 20.7 + - + +
102B MET 3.9 3.8 - - - +
104B ARG* 1.3 73.8 - - - +
106B ASN* 1.3 72.6 + - - +
107B VAL* 3.3 15.6 + - + +
155B LYS* 5.5 0.5 - - - -
156B PRO* 6.0 0.7 - - - +
230B ILE* 4.6 4.9 - - + -
231B ASN* 2.8 39.5 + - - +
234B PHE* 3.4 47.1 - - + +
269B PRO* 3.4 24.2 - - + +
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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