Contacts of the helix formed by residues 97 - 116 (chain D) in PDB entry 1G3I
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 ASP 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C LYS* 5.7 3.3 + - - -
95D GLU* 3.3 18.9 + - - +
96D VAL* 1.3 83.5 - - - +
98D SER* 1.3 62.4 + - - +
99D ILE 3.2 0.3 + - - -
100D ILE* 3.2 8.1 + - - +
101D ARG* 3.1 42.4 + - - +
284D PRO* 5.9 1.0 - - - +
285D LEU* 4.0 14.2 - - - +
291D VAL* 3.6 28.0 - - + +
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Residues in contact with SER 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D LYS* 4.6 8.1 + - - -
86D PHE* 4.1 9.4 - - - -
95D GLU* 2.6 30.6 + - - +
96D VAL 4.0 0.3 + - - -
97D ASP* 1.3 76.3 - - - +
99D ILE* 1.3 61.9 + - - +
101D ARG* 2.7 18.4 + - - +
102D ASP* 2.6 50.2 + - - -
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Residues in contact with ILE 99 (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 ILE* 4.5 5.7 - - + +
81D VAL* 3.8 32.8 - - + -
85D LYS* 6.2 0.2 - - - +
86D PHE* 3.6 33.4 - - + -
96D VAL 3.1 15.0 + - - +
98D SER* 1.3 84.9 + - - +
100D ILE* 1.3 70.0 + - + +
102D ASP* 3.3 7.2 + - - +
103D LEU* 2.9 24.9 + - - +
254D VAL* 3.9 29.2 - - + -
256D ILE* 5.2 3.4 - - + -
282D LEU* 4.0 22.0 - - + -
285D LEU* 4.1 7.9 - - + -
305D PHE* 6.3 0.2 - - + -
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Residues in contact with ILE 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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97D ASP 3.2 3.2 + - - +
98D SER 3.2 0.2 - - - -
99D ILE* 1.3 83.8 - - + +
101D ARG* 1.3 59.2 + - - +
103D LEU* 3.6 9.3 - - + +
104D THR* 2.9 24.0 + - - +
248D VAL* 4.8 8.1 - - + -
254D VAL* 4.6 8.5 - - + -
285D LEU* 3.7 25.4 - - + -
291D VAL* 3.3 20.2 - - + -
293D THR* 3.9 0.2 - - - +
298D VAL* 3.2 31.0 - - + -
300D THR* 3.4 33.4 - - + +
303D ILE* 4.8 3.6 - - + -
305D PHE* 4.5 11.2 - - + -
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Residues in contact with ARG 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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95D GLU* 4.1 22.8 + - - +
97D ASP* 3.1 41.0 + - - +
98D SER* 2.7 24.8 + - - +
100D ILE* 1.3 70.2 - - - +
102D ASP* 1.3 67.9 + - - +
104D THR* 3.2 6.2 + - - -
105D ASP* 3.0 23.9 + - - +
291D VAL* 4.5 4.4 - - + +
292D SER* 3.3 22.9 + - - +
293D THR* 3.8 24.2 - - + +
294D LYS* 5.0 4.0 - - + +
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Residues in contact with ASP 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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79D ILE* 4.6 19.2 - - + +
81D VAL* 5.8 2.8 - - - +
85D LYS* 4.4 12.5 + - - -
98D SER* 2.6 34.2 + - - +
99D ILE* 3.7 5.3 + - - +
101D ARG* 1.3 76.6 - - - +
103D LEU* 1.3 63.2 + - - +
105D ASP* 3.0 14.1 + - - +
106D SER* 2.9 21.5 + - - -
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Residues in contact with LEU 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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77D PRO* 3.6 32.5 - - + +
78D PHE 3.8 3.6 - - - +
79D ILE* 3.2 29.3 - - + +
99D ILE 2.9 17.4 + - - +
100D ILE* 3.6 12.1 - - + +
101D ARG 3.1 0.2 - - - -
102D ASP* 1.3 75.6 - - - +
104D THR* 1.3 64.0 + - - +
106D SER* 2.8 17.6 + - - -
107D ALA* 3.0 11.4 + - - +
248D VAL* 3.5 28.5 - - + -
252D GLY* 4.3 6.7 - - - -
253D ILE 3.9 2.5 - - - +
254D VAL* 3.9 20.6 - - + -
303D ILE* 3.9 13.7 - - + -
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Residues in contact with THR 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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100D ILE 2.9 13.2 + - - -
101D ARG 3.2 8.6 + - - -
103D LEU* 1.3 76.9 - - - +
105D ASP* 1.3 63.1 + - - +
107D ALA* 3.3 1.7 + - - +
108D MET* 2.9 22.7 + - - +
244D ALA* 4.4 10.5 - - + +
245D ILE* 5.0 1.3 - - - -
248D VAL* 3.2 19.1 - - + +
293D THR* 3.3 26.3 - - - +
295D HIS* 3.8 26.2 - - + -
298D VAL* 3.4 21.3 - - + +
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Residues in contact with ASP 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 ARG* 3.0 14.8 + - - +
102D ASP* 3.0 20.7 + - - +
104D THR* 1.3 77.7 - - - +
106D SER* 1.3 59.9 + - - +
108D MET* 3.3 19.3 - - - +
109D LYS* 3.5 4.7 + - - +
294D LYS* 3.2 37.6 + - - +
295D HIS* 3.3 12.4 + - - -
292E SER* 5.1 4.7 - - - -
297E MET* 4.5 27.1 - - + +
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Residues in contact with SER 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D PRO* 4.6 2.5 - - - +
78D PHE 3.9 27.7 + - - -
79D ILE* 5.9 1.3 - - - -
102D ASP 2.9 9.6 + - - -
103D LEU* 2.8 10.5 + - - -
105D ASP* 1.3 73.2 - - - +
107D ALA* 1.3 66.3 + - - -
108D MET 3.0 1.6 - - - -
109D LYS* 2.8 28.5 + - - +
110D LEU* 3.2 7.0 + - - +
297E MET* 6.3 1.1 - - - -
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Residues in contact with ALA 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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77D PRO* 3.3 34.6 - - + +
103D LEU 3.0 5.7 + - - -
104D THR 3.3 2.7 + - - +
106D SER* 1.3 75.5 + - - +
108D MET* 1.3 58.4 + - - +
110D LEU* 3.3 6.3 + - - +
111D VAL* 2.7 33.6 + - - +
244D ALA* 3.6 14.6 - - - +
247D ALA* 3.9 3.8 - - + -
248D VAL* 3.5 25.4 - - + -
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Residues in contact with MET 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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104D THR 2.9 12.0 + - - +
105D ASP 3.3 12.6 - - - +
106D SER 3.0 0.4 - - - -
107D ALA* 1.3 77.7 - - - +
109D LYS* 1.3 52.5 + - - +
111D VAL* 3.7 1.3 - - + +
112D ARG* 2.7 39.7 + - - +
240D LEU* 3.4 29.4 - - + -
241D LYS* 3.2 45.8 - - + +
244D ALA* 3.4 23.1 - - + +
295D HIS* 3.3 36.6 - - + +
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Residues in contact with LYS 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 ASP 3.5 5.1 + - - +
106D SER* 2.8 16.2 + - - +
108D MET* 1.3 75.7 - - - +
110D LEU* 1.3 70.6 + - + +
112D ARG* 2.6 18.6 + - - +
113D GLN* 2.7 43.7 + - + +
299E LYS* 4.3 28.1 - - - +
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Residues in contact with LEU 110 (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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75D ASN* 3.9 33.2 - - - +
76D ALA 3.6 9.6 - - - +
77D PRO* 3.5 42.2 - - + -
106D SER* 3.2 4.8 + - - +
107D ALA* 3.3 11.7 - - - +
109D LYS* 1.3 85.5 - - + +
111D VAL* 1.3 66.8 + - + +
113D GLN* 3.4 21.5 + - - +
114D GLN* 3.0 27.7 + - - +
247D ALA* 6.0 1.3 - - + -
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Residues in contact with VAL 111 (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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107D ALA 2.7 17.5 + - - +
108D MET* 3.7 2.9 - - + +
110D LEU* 1.3 74.6 - - + +
112D ARG* 1.3 57.9 + - - +
114D GLN* 3.3 15.1 + - - +
115D GLU* 3.0 29.5 + - + +
240D LEU* 3.4 28.7 - - + +
243D LYS* 3.8 28.9 - - + -
244D ALA* 3.3 33.2 - - + +
247D ALA* 3.8 15.5 - - + -
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Residues in contact with ARG 112 (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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108D MET* 2.7 22.5 + - - +
109D LYS* 2.6 13.1 + - - +
111D VAL* 1.3 67.4 - - - +
113D GLN* 1.3 57.7 + - + +
114D GLN 2.5 15.9 + - - -
115D GLU* 2.8 13.7 + - - +
116D ILE* 3.0 33.3 + - + +
237D PRO* 5.8 5.1 - - - +
240D LEU* 4.0 35.7 - - + +
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Residues in contact with GLN 113 (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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75D ASN* 5.6 1.4 + - - -
109D LYS* 2.7 46.4 + - + +
110D LEU* 4.1 24.9 + - - +
112D ARG* 1.3 74.9 - - + +
114D GLN* 1.3 58.0 + - - +
116D ILE* 3.4 27.3 - - + +
117D ALA* 4.0 6.4 - - - +
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Residues in contact with GLN 114 (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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75D ASN* 3.6 25.8 + - - +
110D LEU* 3.0 17.0 + - - +
111D VAL* 3.3 17.9 + - - +
112D ARG 2.5 6.5 + - - -
113D GLN* 1.3 77.8 - - - +
115D GLU* 1.3 64.5 + - - +
116D ILE 3.3 2.0 - - - -
117D ALA* 3.7 5.2 + - - +
118D LYS* 3.3 20.8 + - - +
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Residues in contact with GLU 115 (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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111D VAL* 3.0 15.2 + - - +
112D ARG 2.8 4.2 + - - +
114D GLN* 1.3 81.5 + - - +
116D ILE* 1.3 63.0 + - + +
118D LYS* 3.2 36.3 - - + +
119D ASN* 3.4 20.3 + - - +
239D GLU* 6.1 1.1 - - - +
240D LEU* 4.3 16.8 - - + -
243D LYS* 2.9 35.9 + - + +
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Residues in contact with ILE 116 (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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112D ARG* 3.3 39.3 - - + +
113D GLN* 3.4 24.9 - - + +
115D GLU* 1.3 75.7 - - + +
117D ALA* 1.3 89.2 + - + +
118D LYS 3.0 3.8 - - - -
119D ASN* 2.7 31.3 + - - +
120D ARG* 4.7 1.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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