Contacts of the helix formed by residues 107 - 119 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B HIS* 5.0 0.9 + - - -
495B ARG* 2.9 30.5 + - - +
93C ASN 4.4 0.9 - - - +
94C SER* 3.3 6.6 - - - -
95C LEU* 2.8 35.4 + - + +
103C THR* 4.9 0.4 - - + -
104C LEU 3.1 15.9 + - - +
105C LEU 3.1 2.9 + - - +
106C GLU* 1.3 74.6 - - - +
108C PHE* 1.3 55.3 + - - +
109C ILE* 3.2 4.0 + - - +
110C LEU* 2.9 38.6 + - + +
111C ARG* 3.1 31.1 + - - +
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Residues in contact with PHE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A HIS* 5.7 2.9 - - + +
394A GLY* 3.8 22.2 - - - +
395A HIS* 5.7 4.7 - + + -
396A ILE* 3.9 34.3 - - + -
402A PHE* 3.8 16.6 - + + -
412A LEU* 6.0 0.2 - - + -
482A PHE* 4.0 30.3 - + - -
495B ARG* 5.1 3.1 - - - -
82C THR* 4.4 14.4 - - + -
86C VAL* 4.9 7.4 - - + -
106C GLU 2.8 17.9 + - - +
107C ASP* 1.3 70.8 - - - +
109C ILE* 1.3 82.7 + - + +
111C ARG* 3.6 21.8 + - - +
112C GLU* 2.9 32.3 + - + +
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Residues in contact with ILE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A PHE* 4.2 31.2 - - + +
212B HIS* 4.0 15.3 - - + -
495B ARG* 4.0 26.5 - - - +
82C THR* 4.2 12.7 - - + +
86C VAL* 5.6 0.4 - - + -
87C ARG 5.5 0.2 - - - +
88C ILE* 3.7 44.9 - - + -
90C ASP 5.7 1.1 - - - +
107C ASP* 3.2 5.3 + - - +
108C PHE* 1.3 95.8 - - + +
110C LEU* 1.3 65.4 + - - +
112C GLU* 3.9 2.0 - - - +
113C LYS* 3.1 25.2 + - + +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ALA* 4.2 5.8 - - + -
212B HIS* 3.5 48.6 - - - +
410B GLY* 5.0 5.2 - - - -
413B PHE* 6.0 2.2 - - + -
94C SER* 3.8 9.0 - - - +
103C THR* 3.7 29.4 - - + -
107C ASP* 2.9 30.0 + - + +
109C ILE* 1.3 77.3 - - - +
111C ARG* 1.3 68.6 + - + +
113C LYS* 3.3 1.9 + - - +
114C ILE* 2.9 48.5 + - + +
105D LEU* 4.1 15.3 - - + -
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Residues in contact with ARG 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A HIS* 4.9 0.4 + - - -
412A LEU* 2.9 42.0 + - - +
413A PHE* 4.0 11.6 + - - +
416A THR* 4.3 16.4 + - + -
413B PHE* 3.7 42.3 - - + -
104C LEU 5.9 0.7 - - - +
105C LEU* 3.0 45.1 + - - +
106C GLU 4.2 1.2 - - - -
107C ASP 3.1 12.5 + - - +
108C PHE* 3.6 28.4 - - - +
109C ILE 3.4 0.2 - - - -
110C LEU* 1.3 83.4 - - + +
112C GLU* 1.3 55.0 + - - +
115C THR* 2.6 40.0 + - - +
105D LEU* 4.4 7.2 - - + -
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A HIS* 5.5 0.9 + - - -
416A THR* 5.0 12.8 - - + +
428A PHE* 6.4 2.7 - - + -
444A GLN* 3.1 15.9 + - - +
82C THR* 3.3 19.5 - - + +
83C ASN* 2.9 54.7 + - - +
84C GLN* 3.9 14.2 + - - +
108C PHE* 2.9 20.3 + - + +
109C ILE* 3.9 4.1 - - - +
111C ARG* 1.3 75.6 - - - +
113C LYS* 1.3 65.3 + - - +
115C THR* 3.6 5.1 - - - -
116C HIS* 3.0 23.7 + - - +
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Residues in contact with LYS 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A PHE* 6.3 1.8 - - - -
444A GLN* 4.0 25.7 - - + +
212B HIS* 2.9 44.5 + - + +
215B PRO* 4.0 21.1 - - + +
216B ASP* 2.8 35.0 + - - -
88C ILE* 6.5 0.2 - - + -
91C ASP* 3.0 29.0 + - - +
109C ILE* 3.1 15.4 + - + +
110C LEU 3.7 2.7 - - - +
112C GLU* 1.3 81.2 - - - +
114C ILE* 1.3 62.7 + - + +
116C HIS* 3.5 2.8 + - - +
117C PHE* 3.1 21.8 + - - +
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Residues in contact with ILE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ALA* 3.5 25.4 - - + +
212B HIS 4.7 1.8 - - - +
214B PHE* 4.7 0.4 - - + -
215B PRO* 3.7 22.4 - - + -
410B GLY 5.2 2.0 - - - +
413B PHE* 3.8 19.3 - - + -
414B SER* 3.9 12.1 - - - +
760B HDD 4.2 15.3 - - + -
110C LEU* 2.9 38.3 + - + +
113C LYS* 1.3 71.9 - - + +
115C THR* 1.3 60.2 + - - +
117C PHE* 3.2 5.5 + - + +
118C ASP* 2.8 56.8 + - - +
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Residues in contact with THR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A THR* 4.1 21.4 - - + +
417A ASP* 6.0 1.1 - - - -
420A ILE* 3.8 30.5 - - + -
426A PRO* 4.6 3.1 - - + -
428A PHE* 6.1 0.9 - - + -
413B PHE* 3.2 19.0 - - - -
417B ASP* 3.4 13.5 + - - +
111C ARG 2.6 28.9 + - - -
112C GLU* 3.6 7.4 - - - -
114C ILE* 1.3 73.2 - - - +
116C HIS* 1.3 63.4 + - - +
118C ASP 3.2 0.7 + - - -
119C HIS* 3.0 34.6 + - + -
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Residues in contact with HIS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A PRO* 3.5 33.2 - - + +
427A ASN* 2.7 25.0 + - - -
429A HIS* 4.7 0.7 - + - -
444A GLN* 3.0 39.7 - - + +
445A ARG 3.1 37.0 + - - -
446A ASP 3.2 15.9 - - - -
447A GLY 4.5 0.4 - - - -
450A ARG* 3.8 8.6 + - - -
83C ASN* 4.1 6.3 - - - +
112C GLU* 3.0 12.1 + - + +
113C LYS 3.8 4.0 - - - +
115C THR* 1.3 76.0 - - - +
117C PHE* 1.3 65.4 + - - +
119C HIS 3.2 12.1 + - - -
120C GLU* 3.3 14.6 + - - +
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Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A GLN* 5.9 0.2 - - - +
126B ILE* 3.5 36.6 - - + +
127B VAL* 4.3 2.0 - - + -
214B PHE* 3.6 36.3 - + - -
215B PRO* 3.7 32.5 - - + -
218B VAL* 3.5 33.0 - - + -
219B HIS* 4.2 4.0 - + - -
414B SER* 5.2 0.2 - - - -
760B HDD 4.1 15.0 - - + -
113C LYS 3.1 11.8 + - - +
114C ILE* 3.4 11.9 - - + +
116C HIS* 1.3 78.9 + - - +
118C ASP* 1.3 70.1 + - - +
119C HIS 3.1 1.6 + - - -
120C GLU* 3.3 39.2 + - - +
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Residues in contact with ASP 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ILE* 3.3 12.6 - - - +
413B PHE* 3.9 0.7 - - - -
414B SER* 2.6 44.9 + - - -
417B ASP* 2.5 34.5 - - - +
418B THR* 2.7 31.9 + - - -
421B SER* 4.1 2.4 + - - -
760B HDD 3.7 8.3 - - - +
114C ILE* 2.8 31.4 + - - +
115C THR 3.2 2.7 + - - +
117C PHE* 1.3 75.8 - - - +
119C HIS* 1.3 64.2 + - + +
120C GLU 3.6 0.7 - - - -
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Residues in contact with HIS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ILE* 3.7 24.5 - - + +
426A PRO* 3.7 24.1 - - + +
447A GLY* 3.3 15.6 - - - -
448A MET 4.2 1.7 + - - -
126B ILE* 4.5 0.4 - - - -
417B ASP* 2.8 52.5 + - - -
418B THR* 3.9 3.8 - - - -
420B ILE* 4.1 1.1 - - + -
421B SER* 2.6 46.1 + - - +
115C THR* 3.0 31.4 + - + +
116C HIS 3.2 6.0 + - - -
117C PHE 3.2 1.2 - - - -
118C ASP* 1.3 76.6 + - - +
120C GLU* 1.3 62.1 + - - +
121C ARG 3.4 8.7 + - - +
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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