Contacts of the helix formed by residues 107 - 123 (chain A) in PDB entry 1CQ7
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 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A THR* 2.8 31.0 + - - -
106A PRO* 1.3 70.9 - - - +
108A GLY* 1.3 65.5 + - - -
109A THR 3.1 2.2 - - - -
111A ALA* 3.1 7.6 + - - +
266A ARG* 3.4 13.5 + - - -
267A VAL 3.8 10.8 - - - -
268A GLY* 3.8 15.0 - - - -
413A PY5 4.0 9.9 - - - -
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLY* 1.3 70.8 - - - -
109A THR* 1.3 58.0 + - - +
111A ALA* 3.3 5.5 + - - +
112A LEU* 3.1 32.9 + - - +
222A ASP* 5.4 2.1 - - - +
253A ALA* 4.3 2.9 - - - +
254A SER 3.8 19.5 - - - -
255A SER* 3.9 9.8 + - - -
413A PY5 2.9 27.2 + - - -
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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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108A GLY* 1.3 74.5 - - - +
110A GLY* 1.3 60.8 + - - +
112A LEU* 3.2 11.8 + - - +
113A ARG* 3.0 26.9 + - + +
140A TRP* 3.3 19.8 - - + -
142A ASN* 3.8 23.8 - - - +
146A VAL* 4.1 12.8 - - + +
266A ARG* 4.1 8.6 + - - -
413A PY5 2.8 21.4 + - - -
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Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 4.0 6.5 - - - -
106A PRO* 3.4 26.7 + - - -
107A GLY 3.3 4.2 + - - -
109A THR* 1.3 79.8 - - - +
111A ALA* 1.3 57.6 + - - +
113A ARG* 3.4 6.0 + - - +
114A VAL* 2.9 35.8 + - - +
294A ASN* 6.4 0.4 - - - -
295A TYR* 5.8 0.7 - - - -
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Residues in contact with ALA 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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105A THR* 3.3 18.3 + - - +
107A GLY 3.1 8.1 + - - +
108A GLY* 3.4 13.0 - - - +
110A GLY* 1.3 74.7 - - - +
112A LEU* 1.3 64.4 + - - +
114A VAL* 3.2 11.3 - - - +
115A ALA* 3.1 24.3 + - - +
253A ALA* 3.6 13.9 - - + -
269A ALA 3.4 24.7 - - - +
270A CYS* 3.7 4.5 - - + -
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Residues in contact with LEU 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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108A GLY 3.1 19.6 + - - +
109A THR* 3.2 7.8 + - - +
111A ALA* 1.3 77.0 - - - +
113A ARG* 1.3 57.4 + - - +
115A ALA* 3.3 6.4 + - + +
116A ALA* 2.8 29.3 + - - +
140A TRP* 3.9 17.7 - - + -
143A HIS* 3.8 17.7 - - + -
146A VAL* 3.8 17.2 - - + +
147A PHE* 4.2 23.6 - - + -
187A LEU* 4.4 13.2 - - + -
220A LEU* 4.7 7.2 - - + -
222A ASP* 3.7 25.8 - - + +
253A ALA* 3.8 19.3 - - + -
413A PY5 4.7 0.4 - - + -
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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* 3.0 16.7 + - + +
110A GLY* 3.8 7.2 - - - +
112A LEU* 1.3 77.4 - - - +
114A VAL* 1.3 58.3 + - - +
116A ALA* 3.0 3.9 + - - +
117A ASP* 2.8 58.6 + - - +
146A VAL* 3.6 23.2 + - + +
149A SER* 3.4 40.0 + - - -
150A ALA* 4.9 0.7 - - - -
294A ASN* 4.3 18.2 - - - +
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Residues in contact with VAL 114 (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 THR* 4.0 5.8 - - + -
110A GLY* 2.9 20.8 + - - +
111A ALA* 3.2 18.4 - - - +
113A ARG* 1.3 74.9 - - - +
115A ALA* 1.3 60.3 + - - +
117A ASP* 3.5 8.1 + - - +
118A PHE* 2.9 30.3 + - - +
270A CYS* 3.9 19.1 - - + -
287A MET* 4.9 8.5 - - + +
290A ALA* 4.4 6.4 - - + +
291A ILE* 4.0 31.2 - - + +
294A ASN* 4.6 9.4 - - + +
295A TYR* 4.0 22.9 - - + +
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Residues in contact with ALA 115 (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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111A ALA 3.1 19.7 + - - +
112A LEU* 3.4 8.1 - - + +
114A VAL* 1.3 78.8 - - - +
116A ALA* 1.3 57.5 + - - +
118A PHE* 3.3 7.6 + - - +
119A LEU* 2.9 36.1 + - - +
147A PHE* 6.0 0.4 - - + -
220A LEU* 4.7 13.7 - - + -
251A ILE* 4.1 17.7 - - + -
270A CYS* 3.9 15.9 - - - -
287A MET* 4.5 2.7 - - - -
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Residues in contact with ALA 116 (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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112A LEU 2.8 17.9 + - - +
113A ARG* 3.5 8.1 - - - +
115A ALA* 1.3 74.9 - - - +
117A ASP* 1.3 58.8 + - - +
119A LEU* 3.4 5.1 + - - +
120A ALA* 2.9 32.2 + - - +
146A VAL* 4.6 5.8 - - + +
147A PHE* 3.9 24.8 - - + -
150A ALA* 3.6 20.2 - - + -
152A LEU* 3.7 10.2 - - + +
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Residues in contact with ASP 117 (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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113A ARG* 2.8 53.7 + - - +
114A VAL* 3.8 6.2 - - - +
116A ALA* 1.3 73.3 - - - +
118A PHE* 1.3 67.3 + - - +
120A ALA* 4.7 1.1 - - - -
121A LYS* 3.3 53.3 + - - +
122A ASN* 4.4 0.2 + - - -
150A ALA* 3.6 15.4 - - - +
290A ALA* 4.1 18.6 - - + +
294A ASN* 4.4 9.7 + - - +
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Residues in contact with PHE 118 (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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114A VAL 2.9 19.3 + - - +
115A ALA* 3.4 8.3 - - - +
117A ASP* 1.3 78.3 - - - +
119A LEU* 1.3 91.7 + - + +
122A ASN* 2.8 53.8 + - + +
123A THR* 4.9 6.7 - - - -
251A ILE* 4.2 4.9 - - + -
272A LEU* 3.8 27.8 - - + -
283A ALA* 3.5 33.0 - - + -
286A GLN* 4.3 3.1 - - + -
287A MET* 3.9 39.3 - - + -
290A ALA* 4.4 5.1 - - + +
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Residues in contact with LEU 119 (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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115A ALA 2.9 21.5 + - - +
116A ALA* 3.8 7.4 - - - +
118A PHE* 1.3 86.5 - - + +
120A ALA* 1.3 61.9 + - - +
123A THR* 3.0 56.1 + - + +
125A VAL* 4.5 11.1 + - + +
133A VAL* 5.6 4.5 - - + -
147A PHE* 6.0 2.2 - - + -
152A LEU* 5.0 5.2 - - + -
185A VAL* 3.8 24.7 - - + -
218A LEU* 3.9 22.0 - - + -
220A LEU* 4.1 20.9 - - + -
251A ILE* 4.0 11.9 - - + -
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Residues in contact with ALA 120 (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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116A ALA 2.9 19.0 + - - +
117A ASP* 4.2 3.6 - - - +
118A PHE 3.3 0.2 - - - -
119A LEU* 1.3 76.9 - - - +
121A LYS* 1.3 65.7 + - + +
123A THR 4.2 6.5 - - - +
125A VAL 5.0 3.4 - - - +
150A ALA* 3.4 26.7 - - + +
152A LEU* 4.1 20.6 - - + -
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Residues in contact with LYS 121 (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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117A ASP* 3.3 43.5 + - - +
118A PHE 3.3 2.0 + - - -
119A LEU 3.3 0.4 - - - -
120A ALA* 1.3 86.0 - - + +
122A ASN* 1.3 69.9 + - - +
123A THR 3.7 1.6 - - - -
150A ALA* 6.0 1.3 - - - +
290A ALA* 5.3 10.5 + - + +
293A ALA* 5.7 6.3 - - - +
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Residues in contact with ASN 122 (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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117A ASP 4.4 0.2 + - - -
118A PHE* 2.8 51.8 + - + +
121A LYS* 1.3 87.4 - - - +
123A THR* 1.3 62.1 + - - +
286A GLN* 3.0 49.7 + - + +
290A ALA* 5.8 1.0 - - - +
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Residues in contact with THR 123 (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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118A PHE* 4.9 7.4 - - - -
119A LEU* 3.0 39.4 + - + +
120A ALA 4.2 8.5 - - - +
121A LYS 4.8 0.9 - - - -
122A ASN* 1.3 82.7 + - - +
124A SER* 1.3 63.4 + - - +
125A VAL* 3.0 40.0 + - + +
218A LEU* 6.1 0.2 - - + -
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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