Contacts of the helix formed by residues 114 - 129 (chain B) in PDB entry 1GG3
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 ALA 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B SER* 2.6 15.2 + - - +
113B PHE* 1.3 81.9 - - - +
115B THR* 1.3 57.8 + - + +
116B LEU 2.9 2.4 - - - +
117B ALA* 2.8 13.9 + - - +
118B LEU* 2.7 34.0 + - - +
157B LYS* 5.9 3.6 - - - +
161B LEU* 5.4 0.7 - - - +
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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 CYS* 3.4 23.4 - - + +
112B SER* 3.0 21.0 + - - +
114B ALA* 1.3 81.8 - - + +
116B LEU* 1.3 59.9 + - - +
118B LEU* 3.4 13.6 - - + +
119B LEU* 2.9 41.5 + - - +
180B ASN* 6.3 2.0 - - - -
184B LEU* 4.5 8.2 - - + +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 4.0 17.9 - - + -
111B CYS* 3.7 30.5 - - - +
112B SER 2.8 15.3 + - - +
113B PHE* 4.0 13.5 - - + -
115B THR* 1.3 81.7 + - - +
117B ALA* 1.3 58.4 + - - +
119B LEU* 4.3 3.7 - - + +
120B GLY* 3.3 16.6 + - - -
146B LEU* 3.2 30.9 - - + +
147B ALA* 3.7 22.7 - - + -
148B PRO* 4.8 5.2 - - + -
149B ASN* 4.7 6.1 - - - +
154B LEU* 4.6 12.1 - - + +
158B VAL* 4.8 0.5 - - - +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 4.9 1.3 - - + -
114B ALA* 2.8 16.5 + - - +
116B LEU* 1.3 77.8 - - - +
118B LEU* 1.3 60.6 + - - +
120B GLY* 3.1 1.0 + - - -
121B SER* 2.8 29.1 + - - -
154B LEU* 4.1 11.1 - - + +
157B LYS* 3.7 33.2 - - + -
158B VAL* 3.5 21.3 - - + +
161B LEU* 3.7 4.7 - - + +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ALA 2.7 11.9 + - - +
115B THR* 3.4 16.8 - - + +
117B ALA* 1.3 77.2 - - - +
119B LEU* 1.3 64.8 + - + +
121B SER* 2.2 26.6 + - - -
122B TYR* 3.0 35.4 + - + +
161B LEU* 3.9 13.7 - - + +
165B TYR* 3.4 17.3 - - - +
180B ASN* 3.1 39.7 - - + +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 3.6 30.1 - - + -
111B CYS* 4.8 8.5 - - - -
115B THR* 2.9 21.6 + - - +
116B LEU* 4.3 4.7 - - + +
118B LEU* 1.3 78.7 - - + +
120B GLY* 1.3 57.1 + - - +
122B TYR* 3.3 4.1 + - + -
123B THR* 2.8 32.8 + - - -
177B PHE* 3.2 54.4 - - + +
180B ASN* 3.8 19.5 - - + -
181B ALA* 4.1 6.3 - - + +
184B LEU* 4.6 16.8 - - + -
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Residues in contact with GLY 120 (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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116B LEU 3.3 11.2 + - - -
117B ALA 3.1 6.9 + - - -
118B LEU 3.0 1.2 - - - -
119B LEU* 1.3 79.1 - - - +
121B SER* 1.3 51.9 + - - +
123B THR* 2.9 9.6 + - - -
124B ILE* 2.7 37.8 + - - +
146B LEU* 4.2 22.4 - - - -
158B VAL* 4.0 7.4 - - - -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ALA 2.8 9.7 + - - -
118B LEU* 2.2 30.0 + - - +
120B GLY* 1.3 73.1 - - - +
122B TYR* 1.3 59.1 + - - +
124B ILE* 3.3 3.9 + - - +
125B GLN* 2.9 28.9 + - - +
158B VAL* 3.9 14.0 - - - +
161B LEU* 3.5 22.4 - - - +
162B HIS* 4.0 6.7 + - - -
165B TYR* 3.0 37.0 + - - -
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.0 50.8 + - + +
119B LEU* 3.6 7.9 - - + +
121B SER* 1.3 80.3 + - - +
123B THR* 1.3 61.0 + - - +
125B GLN* 3.3 2.8 + - - +
126B SER* 2.8 27.3 + - - -
165B TYR* 3.5 34.5 + + - -
168B MET* 4.0 17.7 - - + -
173B ALA* 3.6 24.0 - - - +
174B ASP* 5.7 0.2 - - - -
176B GLU* 3.4 35.6 + - + +
177B PHE* 4.0 22.9 - - + -
180B ASN* 4.0 10.3 - - - -
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 3.2 54.4 - - - +
119B LEU 2.8 24.4 + - - -
120B GLY* 2.9 11.2 + - - -
122B TYR* 1.3 72.9 - - - +
124B ILE* 1.3 59.4 + - - +
126B SER* 3.3 6.9 + - - -
127B GLU* 3.0 32.5 + - + +
144B PHE* 5.0 3.1 - - + -
146B LEU* 4.5 15.1 - - + +
174B ASP* 5.8 0.2 - - - -
177B PHE* 3.5 12.0 - - - -
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Residues in contact with ILE 124 (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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120B GLY 2.7 22.6 + - - +
121B SER* 3.6 5.4 - - - +
123B THR* 1.3 71.4 - - - +
125B GLN* 1.3 65.8 + - - +
127B GLU* 4.4 1.1 - - - -
128B LEU* 2.8 38.8 + - + +
140B TYR* 4.2 4.5 - - + -
141B VAL* 3.9 22.0 - - + -
144B PHE* 3.6 49.1 - - + -
146B LEU* 4.8 7.2 - - + -
158B VAL* 3.9 8.3 - - + -
162B HIS* 3.5 35.4 - - + +
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B SER 2.9 12.4 + - - +
122B TYR 3.7 5.8 - - - +
123B THR 3.3 0.4 - - - -
124B ILE* 1.3 75.4 - - - +
126B SER* 1.3 58.6 + - - +
129B GLY* 2.7 51.0 + - - +
130B ASP* 3.4 17.9 + - - +
131B TYR 3.9 1.0 - - - +
162B HIS* 2.9 38.4 + - - +
165B TYR* 3.6 21.6 + - + +
168B MET* 3.1 56.9 - - + +
169B THR 6.1 0.2 - - - -
170B PRO* 5.4 1.4 - - - +
173B ALA* 4.0 6.1 - - + -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 6.1 4.0 - - - -
122B TYR 2.8 16.7 + - - -
123B THR* 3.3 10.0 + - - -
125B GLN* 1.3 78.1 - - - +
127B GLU* 1.3 62.5 + - - +
129B GLY* 4.5 1.6 + - - -
170B PRO* 3.8 41.6 - - - +
173B ALA* 3.7 2.7 - - - +
174B ASP* 3.2 26.2 + - - -
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Residues in contact with GLU 127 (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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94B TYR* 4.4 17.8 + - - -
98B LEU* 5.1 1.2 - - - +
101B ARG* 4.1 26.6 + - - +
123B THR* 3.0 23.8 + - + +
124B ILE* 3.9 3.1 - - - +
126B SER* 1.3 81.1 - - - +
128B LEU* 1.3 64.1 + - - +
144B PHE* 3.6 38.1 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 2.8 34.5 + - + +
127B GLU* 1.3 77.6 - - + +
129B GLY* 1.3 63.4 + - - +
130B ASP 4.3 3.8 - - - +
135B LEU* 4.0 21.1 - - + +
140B TYR* 3.4 37.2 - - + +
144B PHE* 3.7 36.3 - - + -
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLN* 2.7 38.6 + - - -
126B SER 4.5 1.5 + - - -
127B GLU 3.7 0.8 - - - -
128B LEU* 1.3 74.1 - - - +
130B ASP* 1.3 67.7 + - - +
162B HIS* 3.2 11.1 + - - -
168B MET 5.8 0.7 - - - -
170B PRO* 6.3 3.4 - - - -
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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