Contacts of the helix formed by residues 100 - 109 (chain D) in PDB entry 2GRA
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 THR 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D GLY 3.5 8.6 + - - -
99D VAL* 1.3 74.4 - - - +
101D ILE* 1.3 71.4 + - - +
102D SER* 3.7 17.7 - - - +
103D SER* 2.7 33.5 + - - -
104D ILE* 3.0 16.0 + - - +
119D ARG* 4.6 3.9 + - - +
164D GLU* 2.9 27.1 - - - +
269D GLN* 3.4 15.5 + - - +
273D ASP* 5.2 0.3 + - - -
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Residues in contact with ILE 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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99D VAL 4.2 0.2 + - - -
100D THR* 1.3 73.3 - - - +
102D SER* 1.3 70.6 + - - +
104D ILE* 2.7 21.5 + - + +
105D GLU* 2.9 37.0 + - + +
117D VAL* 3.5 36.6 - - + +
119D ARG* 3.6 24.6 - - + +
136D ALA* 4.0 4.9 - - + +
137D THR 4.9 1.8 - - - +
138D GLY* 3.9 12.8 - - - -
139D THR* 4.0 7.4 - - - +
164D GLU* 2.8 32.8 + - - +
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Residues in contact with SER 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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100D THR* 3.7 13.1 - - - +
101D ILE* 1.3 79.3 - - - +
103D SER* 1.3 57.0 + - - -
105D GLU* 2.7 36.4 + - - +
106D LYS* 2.9 45.5 + - - +
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Residues in contact with SER 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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79D LEU* 4.2 1.6 - - - +
99D VAL* 4.0 3.3 - - - +
100D THR* 2.7 45.4 + - - -
102D SER* 1.3 79.1 + - - +
104D ILE* 1.3 61.3 + - - +
106D LYS* 3.8 14.6 + - - +
107D LYS* 3.8 15.2 - - - +
269D GLN* 4.6 10.3 + - - -
273D ASP* 5.3 7.6 - - - -
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Residues in contact with ILE 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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68D LEU* 5.3 4.9 - - + -
75D ILE* 5.0 3.6 - - + -
79D LEU* 3.7 19.4 - - + +
92D VAL* 5.7 0.9 - - + -
94D SER* 4.0 24.7 - - - +
99D VAL* 3.4 29.4 - - + +
100D THR 3.0 25.7 + - - +
101D ILE* 2.7 19.4 + - + +
103D SER* 1.3 69.6 - - - +
105D GLU* 1.3 65.7 + - - +
107D LYS* 3.2 17.3 - - - +
108D LEU* 3.4 28.6 - - + +
117D VAL* 4.3 22.0 - - + -
118D ILE 6.0 0.4 - - - +
119D ARG* 5.8 4.3 - - + -
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Residues in contact with GLU 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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101D ILE* 3.4 24.2 - - + +
102D SER* 2.7 18.2 + - - +
104D ILE* 1.3 68.3 - - + +
106D LYS* 1.3 51.5 + - + +
107D LYS 2.3 20.9 + - - -
108D LEU* 2.7 7.3 + - - +
109D SER* 2.6 36.4 + - - +
115D PRO* 3.9 14.9 - - + +
117D VAL* 4.5 15.8 - - + +
138D GLY* 4.3 1.6 - - - -
139D THR* 2.6 50.6 + - - +
140D HIS* 3.8 12.2 + - - +
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Residues in contact with LYS 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 SER* 2.9 37.3 + - - +
103D SER* 3.9 9.5 - - - +
104D ILE 3.4 0.2 - - - -
105D GLU* 1.3 71.8 - - + +
107D LYS* 1.3 67.2 + - - +
109D SER* 4.1 8.5 - - - +
110D ALA* 5.2 1.6 - - - -
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Residues in contact with LYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D PRO* 3.2 21.3 + - - +
79D LEU* 3.3 28.9 - - + -
80D ASP* 2.8 41.8 + - - +
103D SER 3.8 6.7 - - - +
104D ILE 3.2 13.0 - - - +
105D GLU 2.3 19.2 + - - -
106D LYS 1.3 76.5 - - - +
108D LEU* 1.3 60.3 + - - +
109D SER 3.3 1.9 - - - +
110D ALA* 3.4 13.9 - - - +
111D PHE* 3.1 28.8 - - - -
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Residues in contact with LEU 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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79D LEU* 3.6 37.0 - - + +
83D GLY* 3.7 16.2 - - - +
86D ILE* 4.9 17.2 - - + +
92D VAL* 5.1 7.9 - - + -
104D ILE* 3.4 35.9 - - + +
105D GLU* 2.7 3.9 + - - +
107D LYS* 1.3 71.9 - - - +
109D SER* 1.3 65.1 + - - +
110D ALA 3.0 2.0 - - - -
111D PHE* 3.0 20.1 + - + +
112D ARG* 3.1 12.8 + - - +
115D PRO* 3.6 20.3 - - + +
117D VAL* 4.2 16.4 - - + -
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Residues in contact with SER 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 GLU* 2.6 34.7 + - - +
106D LYS* 4.1 7.0 - - - +
108D LEU* 1.3 72.7 - - - +
110D ALA* 1.3 54.1 + - - +
111D PHE 2.7 27.0 + - - +
112D ARG 3.4 8.1 - - - +
113D PRO* 4.3 8.5 - - - +
115D PRO* 4.0 9.1 - - - +
140D HIS* 4.8 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