Contacts of the helix formed by residues 111 - 129 (chain B) in PDB entry 3GA5
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 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B THR* 1.3 72.5 - - - +
112B SER* 1.3 65.4 + - - +
113B LYS* 3.0 45.6 + - - +
114B GLU* 2.9 37.0 + - + +
292B ARG* 3.9 19.9 - - + +
293B VAL 4.6 2.8 + - - -
295B TYR* 3.5 6.9 - - - -
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLU* 4.9 5.9 + - - -
110B THR* 3.4 9.2 + - - -
111B ASP* 1.3 72.5 + - - +
113B LYS* 1.3 62.0 + - - +
114B GLU 3.2 0.2 + - - -
115B SER* 3.2 19.9 + - - -
116B GLY 3.9 2.3 + - - -
153B PRO* 3.9 14.4 - - - +
154B ASP* 2.6 33.9 + - - -
157B ALA* 3.6 23.3 - - - +
158B ARG* 4.4 3.6 - - - +
292B ARG* 5.2 1.0 - - - +
295B TYR* 4.7 0.9 - - - -
401B RGG 4.5 0.9 + - - -
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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
----------------------------------------------------------
111B ASP* 3.0 30.3 + - - +
112B SER* 1.3 79.3 - - - +
114B GLU* 1.3 65.6 + - - +
116B GLY* 3.1 4.3 + - - +
117B VAL* 2.9 28.3 + - + +
157B ALA* 3.8 3.9 - - + +
161B TYR* 3.5 53.1 - - + +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP* 2.9 32.3 + - + +
113B LYS* 1.3 83.3 - - - +
115B SER* 1.3 58.1 + - - +
117B VAL* 3.2 8.1 + - + +
118B ILE* 2.8 47.6 + - + +
293B VAL 4.6 0.2 - - - +
294B PRO* 3.4 13.5 - - - +
295B TYR* 2.7 42.5 + - + +
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B SER 3.2 13.1 + - - -
113B LYS 3.3 0.2 - - - -
114B GLU* 1.3 74.1 - - - +
116B GLY* 1.3 60.6 + - - +
118B ILE* 3.9 1.1 - - - +
119B GLN* 2.9 31.2 + - - +
158B ARG* 3.1 29.5 + - - +
235B VAL* 4.3 11.7 - - - +
254B VAL* 4.1 11.2 - - - +
295B TYR* 3.6 38.2 - - - -
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B SER 3.9 1.6 + - - -
113B LYS 3.1 8.3 + - - -
115B SER* 1.3 78.8 + - - +
117B VAL* 1.3 59.9 + - - +
119B GLN* 3.3 4.9 + - - +
120B GLY* 2.9 25.1 + - - -
158B ARG* 4.1 18.1 - - - +
161B TYR* 4.1 6.3 - - - -
162B VAL* 3.5 28.0 - - - -
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LYS* 2.9 23.8 + - + +
114B GLU* 3.6 9.4 - - - +
116B GLY* 1.3 75.5 - - - +
118B ILE* 1.3 66.1 + - + +
120B GLY 3.2 1.4 + - - -
121B ASP* 3.0 32.0 + - - +
161B TYR* 4.2 21.1 - - + -
165B GLU* 3.5 35.1 - - + +
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 2.8 32.5 + - + +
115B SER 4.0 3.6 - - - +
117B VAL* 1.3 74.6 - - + +
119B GLN* 1.3 59.0 + - - +
121B ASP* 3.3 8.6 + - + +
122B LEU* 2.9 30.5 + - + +
254B VAL* 3.9 11.0 - - + -
295B TYR* 3.6 44.2 - - + +
296B VAL* 4.1 3.4 - - - +
297B GLY* 3.3 33.2 - - - +
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Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER 2.9 19.3 + - - +
116B GLY* 3.8 5.1 - - - +
118B ILE* 1.3 76.7 - - - +
120B GLY* 1.3 57.9 + - - +
122B LEU* 3.2 6.5 + - + +
123B ILE* 2.9 34.5 + - + +
158B ARG* 4.5 7.1 - - - +
162B VAL* 3.4 22.7 - - + +
208B ILE* 3.7 11.9 - - - +
209B ALA 3.0 27.5 + - - +
210B ASN* 5.5 0.9 + - - -
233B PHE* 3.5 28.9 + - + +
234B GLY 3.1 24.6 + - - +
235B VAL* 4.0 7.2 - - + +
253B THR* 6.1 0.4 - - - -
254B VAL* 4.1 10.1 - - + +
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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
----------------------------------------------------------
116B GLY 2.9 15.3 + - - -
117B VAL 3.7 3.8 - - - -
119B GLN* 1.3 76.9 - - - +
121B ASP* 1.3 50.4 + - - +
123B ILE* 3.2 1.5 + - - -
124B ALA* 2.8 35.6 + - - +
162B VAL* 3.7 25.7 - - - +
165B GLU* 4.1 9.9 - - - -
166B LEU* 3.5 10.6 - - - +
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 3.0 22.8 + - - +
118B ILE* 3.6 10.9 - - - +
119B GLN 3.3 0.2 - - - -
120B GLY* 1.3 72.3 - - - +
122B LEU* 1.3 62.4 + - - +
124B ALA* 3.7 5.3 - - - +
125B LYS* 2.9 30.0 + - - +
165B GLU* 2.5 33.3 - - - +
169B LYS* 2.7 26.8 - - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 2.9 20.0 + - + +
119B GLN* 3.7 9.4 - - + +
121B ASP* 1.3 76.5 - - + +
123B ILE* 1.3 64.7 + - - +
125B LYS* 3.2 11.1 + - + +
126B HIS* 2.9 32.0 + - + +
233B PHE* 4.1 12.6 - - + -
252B GLY* 4.6 1.8 - - - -
253B THR* 3.1 36.3 - - - +
254B VAL* 4.3 5.8 - - + -
297B GLY* 4.1 8.1 - - - -
298B VAL 3.8 16.2 - - - +
299B ASP* 3.7 32.3 - - + +
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Residues in contact with ILE 123 (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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119B GLN* 2.9 20.2 + - + +
120B GLY 3.6 3.8 - - - +
122B LEU* 1.3 77.5 - - - +
124B ALA* 1.3 56.7 + - - +
126B HIS* 3.3 1.2 + - - +
127B TRP* 2.8 30.0 + - + +
133B TRP* 5.1 0.8 - - + -
141B ILE* 3.9 17.7 - - + -
162B VAL* 3.7 29.2 - - + -
166B LEU* 3.9 16.8 - - + -
206B VAL* 4.5 8.7 - - + -
208B ILE* 3.7 26.9 - - + -
233B PHE* 3.6 42.1 - - + -
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Residues in contact with ALA 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 2.8 21.2 + - - +
121B ASP 3.7 4.0 - - - +
123B ILE* 1.3 73.3 - - - +
125B LYS* 1.3 63.6 + - - +
127B TRP* 3.4 1.6 + - - +
128B GLN* 3.0 25.1 + - - +
166B LEU* 3.8 5.1 - - + +
169B LYS* 3.6 30.5 - - + -
171B ILE* 3.9 27.9 - - + +
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Residues in contact with LYS 125 (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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121B ASP 2.9 18.1 + - - +
122B LEU* 3.5 11.3 - - + +
124B ALA* 1.3 78.2 - - - +
126B HIS* 1.3 71.9 + - + +
128B GLN* 3.4 15.3 + - - +
129B ALA* 3.3 22.1 + - + +
299B ASP* 2.8 33.3 + - - +
301B ASP* 3.2 26.1 + - - +
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Residues in contact with HIS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 2.9 32.6 + - + +
125B LYS* 1.3 86.2 - - + +
127B TRP* 1.3 60.1 + - - +
129B ALA* 3.4 4.1 + - - +
130B ASN* 2.9 44.9 + - - +
133B TRP* 3.7 22.3 - - + -
233B PHE* 4.1 11.0 - + + -
251B ALA* 3.7 23.6 + - + +
299B ASP* 2.7 38.9 + - + +
300B LYS* 5.1 8.1 - - + -
301B ASP* 5.4 2.9 - - - -
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Residues in contact with TRP 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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123B ILE* 2.8 19.3 + - + +
124B ALA* 3.6 4.0 - - - +
126B HIS* 1.3 74.2 - - - +
128B GLN* 1.3 69.3 + - - +
130B ASN 3.2 18.6 + - - +
131B GLN* 3.8 5.9 + - - +
133B TRP* 3.9 44.5 - + + -
134B ASP* 3.5 37.0 - - + -
139B GLY* 4.4 9.1 + - - -
140B LYS 3.6 17.3 - - - -
141B ILE* 3.7 36.8 - - + -
171B ILE* 3.9 27.6 - - + +
205B GLU* 3.6 15.5 - - - -
206B VAL* 4.4 6.5 - - + -
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Residues in contact with GLN 128 (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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124B ALA 3.0 13.6 + - - +
125B LYS* 3.5 16.8 - - - +
127B TRP* 1.3 83.3 - - + +
129B ALA* 1.3 61.1 + - + +
130B ASN 3.3 0.6 + - - -
131B GLN* 3.9 21.4 + - - +
171B ILE* 6.5 0.2 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS* 3.3 13.2 + - + +
126B HIS* 3.4 6.5 + - - +
127B TRP 3.2 0.6 - - - -
128B GLN* 1.3 79.5 - - + +
130B ASN* 1.3 70.3 + - - +
131B GLN* 3.9 2.2 + - - -
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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
------------------------------------------------------------
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