Contacts of the helix formed by residues 99 - 110 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B GLN* 1.3 70.8 - - - +
100B ARG* 1.3 61.2 + - - +
102B ALA* 2.9 16.4 + - - +
103B GLU* 3.0 16.6 + - - +
216B THR* 5.7 0.2 - - - -
252B THR* 4.7 1.2 - - - -
253B MET 3.6 24.2 + - - -
254B SER* 4.0 3.7 - - - +
1000B PLP 2.7 34.7 + - - -
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Residues in contact with ARG 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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98B GLN* 3.3 21.0 - - - +
99B GLY* 1.3 75.2 - - - +
101B GLY* 1.3 62.4 + - - +
103B GLU* 3.1 14.4 + - - +
104B ASN* 2.9 26.8 + - - +
123B PHE* 4.8 5.9 - - - -
125B THR* 3.4 35.0 - - + +
129B HIS* 3.8 2.8 + - - +
1000B PLP 2.9 41.4 + - - +
71D TYR* 3.9 20.7 + - - -
283D VAL* 2.7 43.5 + - - +
284D VAL 3.9 15.9 - - - +
285D TYR* 4.7 5.6 - - - +
286D GLU 4.4 7.2 - - - -
287D GLY* 3.9 9.5 - - - -
288D MET* 4.5 2.0 - - - +
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Residues in contact with GLY 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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96B THR* 4.0 4.9 - - - -
97B HIS* 4.6 6.5 - - - -
98B GLN* 3.0 13.6 + - - +
100B ARG* 1.3 79.4 - - - +
102B ALA* 1.3 59.0 + - - +
104B ASN* 3.7 6.9 + - - +
105B LEU* 3.4 27.0 + - - +
286B GLU* 3.2 28.8 - - - +
285D TYR 4.8 2.7 + - - -
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Residues in contact with ALA 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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96B THR* 3.8 16.9 + - - +
98B GLN 3.4 3.2 + - - -
99B GLY* 2.9 12.9 + - - +
101B GLY* 1.3 74.7 - - - +
103B GLU* 1.3 60.1 + - - +
105B LEU* 3.2 6.0 + - - +
106B LEU* 2.9 29.3 + - - +
252B THR* 3.9 16.6 - - + -
253B MET 4.6 0.2 - - - +
266B PHE 3.6 27.1 - - - +
267B LEU* 3.7 8.9 - - + +
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Residues in contact with GLU 103 (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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99B GLY 3.0 16.1 + - - +
100B ARG* 3.1 14.9 + - - +
102B ALA* 1.3 72.9 - - - +
104B ASN* 1.3 67.1 + - - +
106B LEU* 3.2 2.5 + - - +
107B SER* 2.8 31.8 + - - +
125B THR* 3.1 21.7 + - - -
126B THR* 3.1 43.6 + - - +
129B HIS* 4.0 9.1 - - + -
214B ASP* 4.1 2.8 - - - +
252B THR* 4.1 23.8 + - + +
1000B PLP 3.1 20.4 - - - -
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Residues in contact with ASN 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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100B ARG 2.9 13.4 + - - +
101B GLY* 3.8 6.4 + - - +
103B GLU* 1.3 76.5 - - - +
105B LEU* 1.3 75.8 + - - +
107B SER* 3.9 1.0 - - - -
108B GLN* 2.9 60.5 + - - +
129B HIS* 3.5 31.2 + - + -
132B LYS* 3.0 17.5 + - - -
285B TYR* 3.8 22.0 - - - +
286B GLU* 5.2 1.8 + - - -
285D TYR* 3.9 14.8 - - + -
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Residues in contact with LEU 105 (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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94B VAL* 4.5 7.9 - - + -
96B THR* 4.0 20.9 - - + -
101B GLY 3.4 13.5 + - - +
102B ALA* 3.2 8.7 + - - +
103B GLU 3.1 0.6 - - - -
104B ASN* 1.3 92.5 - - - +
106B LEU* 1.3 66.0 + - - +
108B GLN* 3.3 3.6 + - - +
109B LEU* 3.1 32.7 + - + +
267B LEU* 4.4 14.4 - - + -
278B ALA* 4.8 3.6 - - - +
281B LEU* 4.1 34.0 - - + +
282B VAL* 4.0 28.3 - - + +
285B TYR* 4.4 7.6 - - + -
286B GLU* 4.7 1.8 - - + -
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Residues in contact with LEU 106 (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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102B ALA 2.9 18.8 + - - +
103B GLU* 4.0 3.4 - - - +
105B LEU* 1.3 73.2 - - - +
107B SER* 1.3 54.1 + - - +
109B LEU* 4.4 6.9 - - - +
110B ALA* 2.7 35.9 + - + +
177B TYR* 4.1 18.8 - - + +
179B CYS* 6.5 0.7 - - - -
212B PHE* 3.6 51.1 - - + -
251B CYS 5.7 0.4 - - - -
252B THR* 3.9 19.1 - - + -
267B LEU* 3.7 15.2 - - + +
274B MET* 3.6 28.0 - - + -
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Residues in contact with SER 107 (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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103B GLU* 2.8 19.4 + - - +
104B ASN 3.9 2.5 - - - -
106B LEU* 1.3 72.4 - - - +
108B GLN* 1.3 65.3 + - - +
109B LEU 3.0 2.1 + - - -
111B ILE* 3.3 37.5 + - - +
126B THR 4.7 1.0 + - - -
129B HIS* 3.4 26.4 + - - +
130B GLN* 3.6 8.1 + - - +
133B ASN* 3.4 22.5 - - - +
177B TYR* 3.8 11.7 + - - -
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Residues in contact with GLN 108 (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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104B ASN* 2.9 38.6 + - - +
105B LEU 3.7 0.2 - - - +
107B SER* 1.3 77.3 - - - +
109B LEU* 1.3 61.4 + - - +
111B ILE 4.6 5.5 - - - +
132B LYS* 3.9 7.9 - - - +
133B ASN* 3.4 23.9 + - - +
281B LEU* 3.6 31.3 - - + +
285B TYR* 3.3 34.2 + - - -
285D TYR* 5.7 0.2 - - - -
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Residues in contact with LEU 109 (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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105B LEU* 3.1 27.2 + - + +
106B LEU* 3.8 6.3 - - - +
107B SER 3.0 0.4 - - - -
108B GLN* 1.3 82.0 - - - +
110B ALA* 1.3 59.5 + - - +
111B ILE 3.6 1.9 - - - +
267B LEU* 4.8 4.3 - - + -
274B MET* 4.5 24.1 - - + +
277B ALA* 3.6 37.7 - - + +
278B ALA* 3.7 29.6 - - + +
281B LEU* 4.0 15.9 - - + -
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Residues in contact with ALA 110 (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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106B LEU* 2.7 24.3 + - + +
109B LEU* 1.3 73.9 - - + +
111B ILE* 1.3 60.9 + - - +
112B LYS* 5.2 3.0 + - - +
115B GLN* 3.8 4.9 - - - +
176B ALA* 3.4 20.2 - - - +
177B TYR* 3.6 24.0 - - + -
210B LYS* 6.3 0.7 - - - +
212B PHE* 4.2 17.3 - - + -
274B MET* 5.3 5.2 - - - -
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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