Contacts of the helix formed by residues 107 - 119 (chain B) in PDB entry 1GGE
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 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B ASN 4.4 0.9 - - - +
94B SER* 3.4 6.2 - - - -
95B LEU* 2.7 37.6 + - + +
104B LEU 3.1 14.6 + - - +
105B LEU 3.1 2.4 + - - -
106B GLU* 1.3 73.3 - - - +
108B PHE* 1.3 57.4 + - - +
109B ILE* 3.3 3.5 + - - +
110B LEU* 3.0 39.6 + - + +
111B ARG* 3.1 32.1 + - - +
212C HIS* 4.9 0.3 + - - -
495C ARG* 2.9 30.1 + - - +
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Residues in contact with PHE 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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82B THR* 4.3 13.5 - - + -
86B VAL* 4.9 6.7 - - + -
106B GLU 2.9 17.5 + - - +
107B ASP* 1.3 72.2 - - - +
109B ILE* 1.3 87.7 + - + +
111B ARG* 3.6 22.6 + - - +
112B GLU* 2.8 32.8 + - + +
495C ARG* 4.9 2.5 - - - -
392D HIS* 5.5 3.6 - - + +
394D GLY* 3.8 22.9 - - - +
395D HIS* 5.6 5.2 - + + -
396D ILE* 4.1 24.2 - - + -
402D PHE* 3.8 20.4 - + + -
412D LEU* 5.9 0.4 - - + -
416D THR* 6.1 0.7 - - - +
482D PHE* 4.0 30.5 - + - -
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Residues in contact with ILE 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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82B THR* 4.1 13.0 - - + -
86B VAL* 5.5 0.4 - - + -
87B ARG 5.4 0.2 - - - +
88B ILE* 3.6 45.1 - - + -
90B ASP 5.7 1.1 - - - +
107B ASP* 3.3 6.0 + - - +
108B PHE* 1.3 108.7 - - + +
110B LEU* 1.3 63.1 + - - +
112B GLU* 3.5 2.9 + - - +
113B LYS* 3.1 24.4 + - + +
212C HIS* 4.0 14.8 - - + -
495C ARG* 3.8 24.5 - - - +
482D PHE* 4.0 25.6 - - + +
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Residues in contact with LEU 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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105A LEU* 4.2 14.4 - - + -
94B SER* 3.7 15.3 - - - +
103B THR* 3.7 24.2 - - + -
104B LEU 5.5 0.2 - - - +
107B ASP* 3.0 29.2 + - + +
109B ILE* 1.3 76.7 - - - +
111B ARG* 1.3 63.7 + - + +
113B LYS* 3.2 2.3 + - - +
114B ILE* 2.9 53.0 + - + +
211C ALA* 4.3 4.3 - - + -
212C HIS* 3.4 51.5 - - + +
410C GLY* 5.1 5.4 - - - -
413C PHE* 6.2 1.6 - - + -
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Residues in contact with ARG 111 (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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105A LEU* 4.4 6.7 - - + -
104B LEU 5.4 0.4 + - - +
105B LEU* 2.9 44.2 + - - +
106B GLU 4.1 1.4 - - - -
107B ASP 3.1 11.8 + - - +
108B PHE* 3.6 27.4 - - - +
109B ILE 3.4 0.2 - - - -
110B LEU* 1.3 85.5 - - + +
112B GLU* 1.3 56.5 + - - +
115B THR* 2.7 39.2 + - - +
413C PHE* 3.7 44.9 - - + -
392D HIS* 5.0 0.2 + - - -
412D LEU* 2.9 43.8 + - - +
413D PHE* 3.8 11.3 + - - +
416D THR* 4.4 14.9 + - + -
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Residues in contact with GLU 112 (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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82B THR* 3.3 18.6 - - + +
83B ASN* 2.9 54.5 + - - +
84B GLN* 3.8 14.2 + - - +
108B PHE* 2.8 23.1 + - + +
109B ILE* 4.0 4.4 - - - +
111B ARG* 1.3 72.8 - - - +
113B LYS* 1.3 57.3 + - - +
115B THR* 3.6 5.4 - - - -
116B HIS* 3.0 29.3 + - - +
395D HIS* 5.7 0.3 + - - -
416D THR* 5.0 13.7 - - + +
428D PHE* 6.3 3.1 - - + -
444D GLN* 3.0 17.4 + - - +
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Residues in contact with LYS 113 (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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88B ILE* 6.3 1.3 - - + -
91B ASP* 3.0 28.1 + - - +
109B ILE* 3.1 17.1 + - + +
110B LEU 3.7 3.4 - - - +
112B GLU* 1.3 77.5 - - - +
114B ILE* 1.3 61.7 + - + +
116B HIS* 3.5 2.3 + - - +
117B PHE* 3.2 22.2 + - - +
212C HIS* 2.9 45.0 + - + +
215C PRO* 4.0 22.2 - - + +
216C ASP* 2.7 34.3 + - - -
443D PHE* 6.4 1.3 - - - -
444D GLN* 3.9 26.6 - - + +
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Residues in contact with ILE 114 (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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110B LEU* 2.9 41.2 + - + +
113B LYS* 1.3 70.8 - - + +
115B THR* 1.3 60.9 + - - +
117B PHE* 3.3 5.6 + - + +
118B ASP* 2.8 55.5 + - - +
211C ALA* 3.6 24.0 - - + +
212C HIS 4.7 2.5 - - - +
215C PRO* 3.6 24.9 - - + -
410C GLY* 5.1 2.9 - - - +
413C PHE* 3.6 22.0 - - + -
414C SER* 3.9 11.9 - - - -
760C HDD 4.3 15.0 - - + -
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Residues in contact with THR 115 (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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111B ARG* 2.7 29.8 + - - +
112B GLU* 3.6 6.3 - - - -
114B ILE* 1.3 74.7 - - - +
116B HIS* 1.3 63.5 + - - +
118B ASP 3.3 0.3 + - - -
119B HIS* 3.0 34.9 + - + -
413C PHE* 3.2 19.8 - - - -
417C ASP* 3.4 15.4 - - - +
416D THR* 4.2 19.9 - - + +
417D ASP* 5.9 1.4 - - - -
420D ILE* 3.8 30.1 - - + -
426D PRO* 4.6 3.1 - - + -
428D PHE* 6.1 0.7 - - + -
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Residues in contact with HIS 116 (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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83B ASN* 4.1 6.7 - - - +
112B GLU* 3.0 11.5 + - + +
113B LYS 3.9 1.3 - - - +
115B THR* 1.3 75.4 - - - +
117B PHE* 1.3 65.4 + - - +
119B HIS* 3.2 12.5 + - - +
120B GLU* 3.3 11.0 + - - +
426D PRO* 3.3 38.3 - - + +
427D ASN* 2.8 25.0 + - - -
429D HIS* 4.5 0.9 - + - -
444D GLN* 3.0 39.3 - - + +
445D ARG 3.1 36.5 + - - -
446D ASP 3.2 15.5 - - - -
450D ARG* 3.8 7.9 + - - -
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Residues in contact with PHE 117 (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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113B LYS 3.2 12.0 + - - +
114B ILE* 3.3 12.1 + - + +
116B HIS* 1.3 79.5 + - - +
118B ASP* 1.3 71.3 + - - +
119B HIS 3.1 1.2 + - - -
120B GLU* 3.2 38.0 + - - +
126C ILE* 3.5 36.9 - - + +
127C VAL* 4.3 2.9 - - + -
214C PHE* 3.5 39.3 - + - -
215C PRO* 3.8 30.1 - - + -
218C VAL* 3.6 32.1 - - + -
219C HIS* 4.3 4.3 - + - -
760C HDD 4.2 14.6 - - + -
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Residues in contact with ASP 118 (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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114B ILE* 2.8 38.1 + - - +
115B THR 3.3 2.2 + - - +
117B PHE* 1.3 75.4 - - - +
119B HIS* 1.3 64.8 + - + +
120B GLU 3.6 0.2 - - - -
126C ILE* 3.3 12.1 - - - +
413C PHE* 3.9 0.3 - - - -
414C SER* 2.6 33.6 + - - -
417C ASP* 2.4 38.0 - - - +
418C THR* 2.7 33.0 + - - -
421C SER* 4.0 2.8 + - - -
760C HDD 3.7 7.4 - - - +
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Residues in contact with HIS 119 (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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115B THR* 3.0 31.4 + - + +
116B HIS 3.2 5.3 + - - -
117B PHE 3.1 1.4 - - - -
118B ASP* 1.3 78.4 + - - +
120B GLU* 1.3 61.1 + - - +
121B ARG 3.4 8.5 + - - +
126C ILE* 4.5 0.4 - - - -
417C ASP* 2.8 53.2 + - - -
418C THR* 3.9 4.0 - - - -
420C ILE* 4.2 0.9 - - + -
421C SER* 2.7 45.5 + - - +
420D ILE* 3.8 24.8 - - + +
426D PRO* 3.6 23.2 - - + +
447D GLY* 3.4 15.1 - - - -
448D MET 4.3 1.7 + - - -
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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