Contacts of the helix formed by residues 99 - 110 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D GLN* 1.3 70.2 - - - +
100D ARG* 1.3 64.4 + - - +
102D ALA* 2.8 16.2 + - - +
103D GLU* 2.9 19.1 + - - +
216D THR* 5.8 0.4 - - - -
252D THR* 4.6 1.4 - - - -
253D MET 3.6 23.3 + - - -
254D SER* 4.0 5.3 - - - +
1000D PLP 2.7 28.9 + - - -
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B TYR* 3.8 22.0 + - - -
283B VAL* 2.9 40.2 + - - +
284B VAL 4.1 14.8 - - - +
285B TYR 4.5 5.4 - - - +
286B GLU 4.4 6.3 - - - -
287B GLY* 3.9 14.0 - - - +
288B MET* 4.5 1.6 - - - +
98D GLN* 3.2 20.6 - - + +
99D GLY* 1.3 75.0 - - - +
101D GLY* 1.3 58.5 + - - +
103D GLU* 2.9 14.1 + - - +
104D ASN* 2.8 31.8 + - - +
123D PHE* 5.0 5.3 - - - -
125D THR* 3.4 38.2 - - + +
129D HIS* 4.0 3.0 + - - +
1000D PLP 2.8 56.5 + - - +
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Residues in contact with GLY 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B TYR 4.7 5.0 + - - -
96D THR* 3.9 6.7 - - - -
97D HIS* 4.7 4.0 - - - -
98D GLN* 3.3 12.1 + - - +
99D GLY 3.1 1.0 - - - -
100D ARG* 1.3 79.7 - - - +
102D ALA* 1.3 58.3 + - - +
104D ASN* 3.7 7.9 + - - +
105D LEU* 3.4 28.4 + - - +
286D GLU* 3.3 25.7 - - - +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D THR* 3.7 17.6 + - - +
98D GLN 3.4 3.8 + - - +
99D GLY* 2.8 13.0 + - - +
101D GLY* 1.3 76.5 - - - +
103D GLU* 1.3 62.9 + - - +
105D LEU* 3.4 5.8 + - - +
106D LEU* 3.1 24.4 + - - +
252D THR* 3.8 14.1 - - - +
266D PHE 3.6 28.0 - - - +
267D LEU* 3.9 9.8 - - + +
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Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D GLY 2.9 16.4 + - - +
100D ARG* 2.9 12.0 + - - +
102D ALA* 1.3 74.0 - - - +
104D ASN* 1.3 66.2 + - - +
105D LEU 3.1 0.2 + - - -
106D LEU* 3.2 3.5 + - - +
107D SER* 2.9 30.4 + - - +
125D THR* 2.8 27.2 + - - +
126D THR* 2.9 43.2 + - - +
129D HIS* 4.1 9.2 - - + -
214D ASP* 4.0 4.5 - - - +
252D THR* 4.1 20.9 + - + +
1000D PLP 3.2 18.4 + - - -
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Residues in contact with ASN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B TYR* 4.0 12.9 - - + -
100D ARG 2.8 18.2 + - - +
101D GLY* 3.7 7.6 + - - +
103D GLU* 1.3 74.0 - - - +
105D LEU* 1.3 70.5 + - - +
107D SER* 3.8 1.4 - - - -
108D GLN* 2.8 56.2 + - - +
129D HIS* 3.6 26.2 + - + +
132D LYS* 2.9 19.6 + - - +
285D TYR* 3.7 30.1 - - - +
286D GLU* 5.3 1.8 + - - -
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D VAL* 4.8 3.8 - - + -
96D THR* 3.8 21.3 - - + -
101D GLY 3.4 16.1 + - - +
102D ALA* 3.5 7.9 - - - +
103D GLU 3.1 0.4 - - - -
104D ASN* 1.3 96.6 - - - +
106D LEU* 1.3 62.6 + - - +
108D GLN* 3.1 4.9 + - - +
109D LEU* 3.0 31.8 + - + +
267D LEU* 4.3 18.2 - - + -
278D ALA 4.8 3.8 - - - +
281D LEU* 4.1 27.8 - - + +
282D VAL* 4.1 32.3 - - + +
285D TYR* 4.4 10.3 - - + -
286D GLU* 4.7 1.6 - - + -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ALA 3.1 14.5 + - - +
103D GLU* 3.9 2.9 - - - +
105D LEU* 1.3 78.7 - - - +
107D SER* 1.3 57.8 + - - +
109D LEU* 4.5 6.7 - - - +
110D ALA* 2.8 33.2 + - + +
177D TYR* 4.2 17.7 - - + +
179D CYS* 6.4 0.9 - - - -
212D PHE* 3.6 56.5 - - + -
252D THR* 3.8 21.5 - - + +
267D LEU* 3.8 14.3 - - + +
274D MET* 3.6 22.7 - - + -
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLU* 2.9 18.6 + - - +
104D ASN 3.8 2.7 - - - -
106D LEU* 1.3 77.0 - - - +
108D GLN* 1.3 62.2 + - - +
111D ILE* 3.2 44.2 + - - +
126D THR 4.7 0.9 + - - -
129D HIS* 3.3 40.5 + - - +
130D GLN* 3.6 4.5 + - - +
133D ASN* 3.4 10.4 - - - +
177D TYR* 3.8 8.7 + - - -
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Residues in contact with GLN 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B TYR* 5.7 0.2 - - - -
104D ASN* 2.8 43.3 + - - +
105D LEU 3.1 5.5 + - - +
107D SER* 1.3 76.9 - - - +
109D LEU* 1.3 60.3 + - - +
111D ILE 4.4 7.3 - - - +
132D LYS* 3.9 5.3 - - - +
133D ASN* 3.3 26.5 - - - +
281D LEU* 3.6 27.0 - - + +
285D TYR* 3.6 28.3 + - - -
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LEU* 3.0 26.1 + - + +
106D LEU* 3.8 6.3 - - - +
108D GLN* 1.3 81.1 - - - +
110D ALA* 1.3 59.7 + - + +
111D ILE 3.7 0.7 - - - -
267D LEU* 4.9 1.8 - - + -
269D MET* 4.8 1.1 - - + -
274D MET* 4.0 28.7 - - + +
277D ALA* 3.3 39.7 - - + +
278D ALA* 3.6 32.1 - - + +
281D LEU* 4.4 12.3 - - + -
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 2.8 22.1 + - + +
109D LEU* 1.3 74.7 - - + +
111D ILE* 1.3 60.9 + - - +
112D LYS* 5.1 3.7 + - - +
115D GLN* 3.9 4.2 - - - +
176D ALA* 3.6 20.8 - - - +
177D TYR* 3.8 21.3 - - + -
210D LYS* 6.2 1.8 - - + +
212D PHE* 4.2 16.4 - - + -
274D MET* 5.1 5.8 - - + -
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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