Contacts of the helix formed by residues 99 - 110 (chain A) in PDB entry 1C7G
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 GLY 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLN* 1.3 69.8 - - - +
100A ARG* 1.3 63.7 + - - +
102A ALA* 3.0 15.7 + - - +
103A GLU* 3.1 16.2 + - - +
216A THR* 5.7 0.2 - - - -
252A THR* 4.7 1.7 - - - -
253A MET 3.8 20.6 - - - -
254A SER* 4.0 5.5 - - - +
1000A PLP 2.7 35.3 + - - -
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Residues in contact with ARG 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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98A GLN* 3.2 21.4 - - - +
99A GLY* 1.3 72.5 - - - +
101A GLY* 1.3 61.9 + - - +
103A GLU* 3.1 14.6 + - - +
104A ASN* 2.8 29.8 + - - +
123A PHE* 4.8 6.5 - - - -
125A THR* 3.5 34.7 - - + +
129A HIS* 3.8 4.1 + - - +
1000A PLP 2.8 47.8 + - - +
71C TYR* 3.8 20.4 + - - -
283C VAL* 2.8 41.9 + - - +
284C VAL 3.6 16.8 - - - +
285C TYR* 4.5 3.1 - - - +
286C GLU 4.3 7.6 - - - -
287C GLY* 3.9 11.2 - - - -
288C MET* 4.5 2.4 - - - +
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Residues in contact with GLY 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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96A THR* 4.0 6.5 - - - -
97A HIS* 4.6 6.5 - - - -
98A GLN 3.4 8.6 + - - -
99A GLY 3.2 0.8 - - - -
100A ARG* 1.3 79.2 - - - +
102A ALA* 1.3 62.5 + - - +
104A ASN* 3.5 8.5 + - - +
105A LEU* 3.3 25.8 + - - +
286A GLU* 3.4 26.5 - - - +
285C TYR 4.5 5.1 + - - -
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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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96A THR* 3.7 19.2 + - - +
98A GLN 3.6 4.4 + - - +
99A GLY* 3.0 11.3 + - - +
101A GLY* 1.3 75.0 - - - +
103A GLU* 1.3 59.4 + - - +
105A LEU* 3.1 7.5 + - - +
106A LEU* 2.9 29.6 + - - +
252A THR* 4.1 13.1 - - + +
253A MET 4.7 0.9 - - - +
266A PHE* 3.7 27.8 - - - +
267A LEU* 4.0 11.2 - - + +
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Residues in contact with GLU 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 GLY 3.1 16.8 + - - +
100A ARG* 3.5 14.3 - - - +
102A ALA* 1.3 72.9 - - - +
104A ASN* 1.3 66.8 + - - +
106A LEU* 4.1 2.0 - - - +
107A SER* 2.9 32.0 + - - +
125A THR* 2.8 23.9 + - - -
126A THR* 3.0 43.4 + - - +
129A HIS* 4.0 10.3 - - + -
214A ASP* 4.0 2.4 - - - +
252A THR* 4.1 24.9 + - + +
1000A PLP 3.1 19.5 - - - -
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Residues in contact with ASN 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 ARG 2.8 16.1 + - - +
101A GLY* 3.6 7.9 + - - +
103A GLU* 1.3 76.8 - - - +
105A LEU* 1.3 68.1 + - - +
107A SER* 4.0 1.0 - - - -
108A GLN* 2.7 56.1 + - - +
129A HIS* 3.6 24.6 + - + -
132A LYS* 2.8 21.2 + - - +
285A TYR* 3.6 37.2 - - - +
286A GLU* 5.4 2.0 + - - -
285C TYR* 4.0 12.0 - - + -
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Residues in contact with LEU 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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94A VAL* 4.6 6.3 - - + -
96A THR* 3.8 22.2 - - + -
101A GLY 3.3 16.4 + - - +
102A ALA* 3.1 8.2 + - - +
104A ASN* 1.3 89.5 - - - +
106A LEU* 1.3 67.5 + - - +
108A GLN* 3.2 3.8 + - - +
109A LEU* 3.1 31.4 + - + +
267A LEU* 4.2 14.1 - - + -
278A ALA 4.8 3.8 - - - +
281A LEU* 4.0 37.9 - - + +
282A VAL* 4.0 27.8 - - + +
285A TYR* 4.3 6.7 - - + -
286A GLU* 4.6 2.0 - - + -
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Residues in contact with LEU 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 ALA 2.9 19.2 + - - +
103A GLU* 4.1 3.1 - - - +
105A LEU* 1.3 72.5 - - - +
107A SER* 1.3 57.8 + - - +
109A LEU* 3.1 6.7 + - - +
110A ALA* 2.8 32.6 + - + +
177A TYR* 3.9 22.9 - - + +
179A CYS* 6.5 0.4 - - - -
212A PHE* 3.8 46.9 - - + -
252A THR* 3.9 19.5 - - + -
267A LEU* 3.9 17.2 - - + +
274A MET* 3.7 27.6 - - + -
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Residues in contact with SER 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 GLU* 2.9 20.5 + - - +
104A ASN 4.0 0.7 - - - -
106A LEU* 1.3 76.6 - - - +
108A GLN* 1.3 62.6 + - - +
109A LEU 3.3 0.3 + - - -
111A ILE* 3.4 37.9 + - - +
126A THR 4.7 1.4 + - - -
129A HIS* 3.5 26.0 - - - +
130A GLN* 3.8 4.9 + - - +
133A ASN* 3.4 22.8 - - - +
177A TYR* 3.8 14.4 + - - -
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Residues in contact with GLN 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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104A ASN* 2.7 45.0 + - - +
105A LEU 3.7 0.2 - - - +
107A SER* 1.3 76.5 - - - +
109A LEU* 1.3 61.7 + - - +
111A ILE 4.5 6.5 - - - +
132A LYS* 3.9 6.8 - - - +
133A ASN* 3.4 25.0 + - - +
281A LEU* 3.6 31.1 - - + +
285A TYR* 3.4 33.2 + - - -
285C TYR* 5.5 1.0 + - - -
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Residues in contact with LEU 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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105A LEU* 3.3 24.2 - - + +
106A LEU* 3.1 6.1 + - - +
108A GLN* 1.3 82.2 - - - +
110A ALA* 1.3 60.1 + - - +
111A ILE 3.7 1.5 + - - +
267A LEU* 4.9 0.7 - - + -
269A MET* 4.9 0.9 - - + -
274A MET* 4.2 28.3 - - + +
277A ALA* 3.5 35.4 - - + +
278A ALA* 3.6 32.3 - - + +
281A LEU* 4.1 16.6 - - + -
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Residues in contact with ALA 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 LEU* 2.8 24.5 + - + +
109A LEU* 1.3 74.1 - - - +
111A ILE* 1.3 60.5 + - - +
112A LYS* 5.3 2.2 + - - +
115A GLN* 4.0 3.1 - - - +
176A ALA* 3.4 21.4 - - - +
177A TYR* 3.7 23.3 - - + -
210A LYS* 6.2 1.3 - - - +
212A PHE* 4.4 15.7 - - + -
274A MET* 4.7 7.6 - - - -
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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