Contacts of the helix formed by residues 102 - 113 (chain A) in PDB entry 1XTG
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 ASP 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A THR* 1.3 73.3 - - - +
103A LEU* 1.3 63.6 + - - +
105A ARG* 2.6 36.5 + - - +
106A MET* 2.9 28.1 + - - +
357A PHE* 4.5 2.7 - - + -
157B ILE* 3.7 36.7 - - + +
160B LEU* 3.9 17.4 - - + +
161B ARG* 5.6 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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101A THR* 3.2 7.3 + - - +
102A ASP* 1.3 80.3 - - - +
104A GLY* 1.3 57.4 + - - +
106A MET* 3.4 2.3 + - - +
107A LEU* 3.0 26.9 + - - +
348A ILE* 3.7 36.8 - - + +
349A TYR* 3.9 12.4 - - + -
353A ASN* 3.6 40.2 - - + +
354A PHE* 3.6 29.4 - - + +
357A PHE* 3.7 23.5 - - + -
156B ILE* 4.6 4.3 - - + -
160B LEU* 3.8 12.6 - - + +
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Residues in contact with GLY 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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98A ILE* 3.1 28.0 - - - -
101A THR* 3.3 7.7 + - - -
103A LEU* 1.3 78.1 - - - +
105A ARG* 1.3 65.1 + - - +
107A LEU* 3.2 1.6 + - - +
108A LEU* 3.0 30.2 + - - +
354A PHE* 3.6 18.5 - - - -
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Residues in contact with ARG 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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98A ILE 3.9 0.8 + - - -
99A TYR* 3.0 77.3 + - + +
100A SER* 3.6 17.0 + - - +
101A THR* 3.0 14.4 + - - +
102A ASP* 2.6 42.3 + - - +
104A GLY* 1.3 75.3 - - - +
106A MET* 1.3 63.0 + - - +
108A LEU* 3.6 2.4 + - - +
109A THR* 2.9 30.4 + - - +
387A TYR* 5.7 1.4 + - - -
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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 ASP 2.9 17.9 + - - +
103A LEU 3.7 4.0 - - - +
105A ARG* 1.3 76.1 - - - +
107A LEU* 1.3 60.0 + - - +
109A THR* 3.3 6.4 + - - -
110A SER* 2.9 26.3 + - - +
344A MET* 4.3 4.9 - - + -
349A TYR* 3.0 23.2 + - + +
160B LEU* 3.7 38.1 - - + +
163B MET 4.7 0.9 - - - -
164B ALA* 4.1 14.4 - - - +
167B MET* 3.1 49.1 - - + +
168B GLY* 3.6 10.8 - - - +
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 5.2 2.2 - - + -
103A LEU 3.0 17.6 + - - +
104A GLY 3.7 3.8 - - - +
106A MET* 1.3 76.7 - - - +
108A LEU* 1.3 58.8 + - + +
110A SER* 3.2 3.5 + - - -
111A ILE* 2.9 43.7 + - + +
222A ALA* 4.3 1.8 - - + +
225A LEU* 3.8 36.6 - - + +
226A ILE* 4.2 11.7 - - + -
229A GLY* 5.1 4.9 - - - -
349A TYR* 3.5 37.0 + - + -
354A PHE* 3.6 29.6 - - + -
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Residues in contact with LEU 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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2A PRO* 3.5 40.4 - - + -
42A ILE* 5.1 3.1 - - + -
95A PHE* 3.7 41.5 - - + +
98A ILE* 3.8 19.1 - - + -
99A TYR* 4.1 12.1 - - + -
104A GLY 3.0 20.8 + - - +
105A ARG* 4.0 3.6 - - - +
107A LEU* 1.3 75.1 - - + +
109A THR* 1.3 57.2 + - - +
111A ILE* 3.3 12.6 + - + +
112A VAL* 2.9 34.4 + - - +
225A LEU* 4.0 17.0 - - + -
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Residues in contact with THR 109 (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 PRO* 4.9 1.6 - - - +
99A TYR* 6.0 1.4 - - - -
105A ARG* 2.9 20.0 + - - +
106A MET* 3.6 8.2 - - - -
108A LEU* 1.3 74.5 - - - +
110A SER* 1.3 60.3 + - - +
112A VAL* 3.3 6.5 + - - +
113A ARG* 2.9 35.5 + - + +
167B MET 3.2 26.2 - - - +
168B GLY 3.8 19.3 + - - +
169B ASN 4.0 15.5 - - - +
170B GLU* 4.3 13.9 + - + +
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Residues in contact with SER 110 (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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106A MET* 2.9 8.2 + - - +
107A LEU* 3.2 9.8 + - - -
109A THR* 1.3 76.7 - - - +
111A ILE* 1.3 58.4 + - - +
113A ARG* 3.3 6.1 + - - +
114A GLY 2.9 13.5 + - - -
229A GLY* 6.4 0.7 - - - -
233A TYR* 2.7 34.0 + - - -
341A LEU* 5.7 0.4 - - - +
344A MET* 3.7 11.4 - - - +
345A LEU* 4.4 10.4 - - - +
349A TYR* 2.8 36.0 + - - -
167B MET* 4.9 7.9 + - - +
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Residues in contact with ILE 111 (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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42A ILE* 4.6 9.9 - - + -
107A LEU* 2.9 28.9 + - + +
108A LEU* 3.5 13.2 - - + +
110A SER* 1.3 75.6 - - - +
112A VAL* 1.3 62.9 + - - +
114A GLY* 3.1 7.1 + - - -
150A ASN* 2.9 22.8 + - + -
151A LEU* 4.4 22.4 - - + -
225A LEU* 3.5 51.1 - - + +
228A ALA* 4.7 2.9 - - + -
229A GLY* 4.3 12.6 - - - -
232A LEU* 3.8 22.5 - - + +
233A TYR* 5.1 1.6 - - - -
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Residues in contact with VAL 112 (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 PRO* 4.1 2.5 - - + -
39A HIS* 3.8 16.4 - - + +
40A ASN* 3.7 20.9 - - + +
41A LYS* 3.8 14.9 - - + +
42A ILE* 4.1 15.3 - - + -
108A LEU 2.9 21.2 + - - +
109A THR 3.3 4.0 + - - +
111A ILE* 1.3 76.2 - - - +
113A ARG* 1.3 57.6 + - - +
115A ILE* 4.1 7.1 - - - +
150A ASN* 3.0 17.5 + - - +
170B GLU* 3.6 45.3 - - + +
171B ILE* 5.1 4.3 - - - +
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Residues in contact with ARG 113 (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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109A THR* 2.9 24.7 + - - +
110A SER* 4.6 1.6 - - - +
112A VAL* 1.3 75.3 - - - +
114A GLY* 1.3 58.4 + - - +
115A ILE* 2.8 14.8 + - - +
233A TYR* 3.5 11.2 - - - +
319A GLU* 3.2 25.1 + - - +
320A LYS* 3.7 10.5 - - - +
322A LEU* 4.5 0.2 - - - +
166B ASP 2.7 25.6 + - - -
167B MET* 2.8 52.8 + - - +
169B ASN* 2.6 35.0 + - - +
170B GLU* 4.1 9.4 - - - -
171B ILE* 3.6 46.2 - - + +
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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