Contacts of the helix formed by residues 140 - 157 (chain C) in PDB entry 6GR2
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 SER 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C GLY* 4.2 2.8 - - - -
37C ARG* 2.9 28.3 + - - +
133C VAL* 4.3 0.4 - - - -
138C GLY* 3.2 6.3 - - - +
139C LEU* 1.3 95.6 + - - +
141C SER* 1.3 66.8 + - - +
142C SER* 3.1 8.5 - - - +
143C ALA* 4.0 8.6 - - - +
144C SER* 3.1 19.9 + - - -
186C ASP* 3.9 33.4 - - - -
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Residues in contact with SER 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C THR* 4.6 1.6 + - - -
131C SER* 5.2 1.3 - - - -
133C VAL* 3.7 24.3 - - - +
134C PRO 4.0 6.2 + - - -
135C LEU* 3.5 41.4 - - - +
136C GLY 3.8 6.2 + - - -
139C LEU 3.5 2.0 - - - -
140C SER* 1.3 75.2 - - - +
142C SER* 1.3 59.4 + - - +
144C SER* 3.2 6.3 + - - -
145C LEU* 2.8 31.4 + - - +
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Residues in contact with SER 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C TYR* 3.6 34.8 - - - -
140C SER* 4.5 6.6 - - - -
141C SER* 1.3 81.4 + - - +
143C ALA* 1.3 67.2 + - - +
145C LEU* 3.2 7.5 + - - +
146C GLU* 2.9 37.3 + - - +
174C GLU* 3.4 18.2 + - - -
186C ASP* 5.5 1.6 + - - -
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Residues in contact with ALA 143 (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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140C SER* 3.5 9.3 + - - -
141C SER 3.4 0.2 - - - -
142C SER* 1.3 83.7 + - - +
144C SER* 1.3 57.3 + - - +
146C GLU* 3.5 11.0 - - - -
147C VAL* 2.9 37.2 + - - +
186C ASP* 3.7 44.6 - - + +
187C GLN* 3.9 12.8 - - - +
190C SER* 4.5 3.4 - - - -
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Residues in contact with SER 144 (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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34C ALA* 2.6 28.7 + - - +
35C PRO 3.7 20.9 + - - -
36C GLY 4.1 1.3 + - - -
60C MET 4.1 0.7 - - - -
61C THR* 2.6 22.1 + - - -
133C VAL* 4.2 3.8 - - - +
140C SER 3.1 15.8 + - - -
141C SER* 3.4 13.0 - - - -
143C ALA* 1.3 77.1 - - - +
145C LEU* 1.3 62.1 + - - +
148C ALA* 3.0 26.5 + - - +
190C SER* 4.2 3.6 - - - -
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Residues in contact with LEU 145 (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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61C THR* 4.0 9.3 + - + +
63C LEU* 5.2 2.7 - - + -
106C TRP* 4.0 31.4 - - + +
109C TYR* 4.1 18.6 - - + -
110C VAL* 4.6 11.0 - - + -
129C VAL* 3.6 40.4 - - + -
141C SER 2.8 19.7 + - - +
142C SER* 3.6 5.4 - - - +
144C SER* 1.3 72.5 - - - +
146C GLU* 1.3 58.2 + - - +
148C ALA* 3.4 0.7 + - - +
149C THR* 2.8 43.4 + - - +
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Residues in contact with GLU 146 (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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109C TYR* 3.0 40.0 - - + +
113C VAL* 3.7 21.4 - - + +
142C SER 2.9 20.6 + - - +
143C ALA* 3.5 7.0 - - - +
145C LEU* 1.3 76.7 - - - +
147C VAL* 1.3 57.6 + - - +
149C THR* 3.2 5.4 + - - -
150C TYR* 2.9 23.2 + - - +
170C CYS* 3.5 29.5 - - + +
173C ALA* 5.5 0.7 - - + -
174C GLU* 2.6 36.3 - - - +
187C GLN* 3.3 16.8 + - - +
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Residues in contact with VAL 147 (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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34C ALA* 4.2 1.3 - - + -
143C ALA 2.9 20.6 + - - +
146C GLU* 1.3 72.9 - - - +
148C ALA* 1.3 57.5 + - - +
150C TYR* 3.2 1.8 + - + +
151C THR* 2.7 37.1 + - - -
170C CYS* 3.9 19.5 - - + -
187C GLN* 3.9 21.3 - - + +
190C SER* 3.8 25.4 - - - +
191C LEU* 3.4 33.9 - - + -
387C ALA* 3.6 20.0 - - + -
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Residues in contact with ALA 148 (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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32C VAL* 3.3 25.7 - - + +
34C ALA* 3.5 15.3 - - + +
61C THR* 3.9 22.4 - - + +
63C LEU* 4.3 9.0 - - + -
144C SER 3.0 19.5 + - - +
145C LEU 3.6 3.6 - - - +
147C VAL* 1.3 77.2 - - - +
149C THR* 1.3 62.8 + - - +
151C THR* 3.2 2.8 + - - -
152C PHE* 2.9 20.6 + - - +
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Residues in contact with THR 149 (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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63C LEU* 4.1 18.6 - - + +
110C VAL* 3.7 33.6 - - + +
113C VAL* 3.5 28.3 - - + -
114C ILE* 4.9 1.3 - - + -
125C PHE* 5.7 4.0 - - + -
145C LEU* 2.8 23.4 + - - +
146C GLU 3.4 9.2 - - - -
148C ALA* 1.3 75.2 - - - +
150C TYR* 1.3 63.1 + - - +
152C PHE* 3.1 5.3 + - + +
153C LEU* 3.0 33.1 + - + +
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Residues in contact with TYR 150 (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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113C VAL* 3.9 9.6 - - + -
117C TYR* 3.5 27.1 - + - -
118C PRO* 3.6 20.0 - - + +
146C GLU 2.9 13.9 + - - +
147C VAL* 3.2 9.4 + - + +
149C THR* 1.3 76.5 - - - +
151C THR* 1.3 64.3 + - - +
153C LEU* 3.2 6.6 + - - +
154C GLN* 3.1 32.7 + - - +
159C ASP* 2.8 23.7 + - - -
165C ALA* 5.1 1.4 - - - +
166C ARG* 3.2 39.0 + - + +
169C VAL* 3.6 37.9 - - + +
170C CYS* 3.8 17.5 - - - -
191C LEU* 5.7 2.7 - - + -
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Residues in contact with THR 151 (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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32C VAL* 3.2 28.0 - - + -
147C VAL* 2.7 27.3 + - - +
148C ALA* 3.7 3.1 - - - -
150C TYR* 1.3 74.5 - - - +
152C PHE* 1.3 61.6 + - - +
154C GLN* 3.3 30.4 + - - +
155C GLN* 3.5 10.3 + - - +
191C LEU* 5.0 2.8 - - - +
387C ALA* 3.5 18.8 - - + +
388C LYS* 4.3 20.2 - - - +
389C VAL* 4.4 9.4 - - + -
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Residues in contact with PHE 152 (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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30C LEU* 3.8 24.5 - - + -
32C VAL* 3.9 11.1 - - + +
63C LEU* 3.5 31.0 - - + -
65C GLY* 3.8 40.2 - - - -
66C SER 3.9 3.8 - - - -
125C PHE* 3.1 42.4 - + + -
148C ALA 2.9 13.6 + - - +
149C THR* 3.4 10.3 - - + +
151C THR* 1.3 74.8 - - - +
153C LEU* 1.3 64.0 + - + +
155C GLN* 2.8 29.8 + - + +
156C LEU* 3.3 29.7 + - + +
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Residues in contact with LEU 153 (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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113C VAL* 4.0 21.5 - - + -
114C ILE* 4.0 22.7 - - + -
117C TYR* 3.6 35.0 - - + -
122C LEU* 4.1 17.5 - - + -
125C PHE* 4.1 32.1 - - + -
149C THR* 3.0 19.7 + - + +
150C TYR 3.7 5.6 - - - +
152C PHE* 1.3 83.0 - - + +
154C GLN* 1.3 56.6 + - - +
156C LEU* 3.2 12.5 + - + +
157C CYS* 2.7 32.7 + - - +
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Residues in contact with GLN 154 (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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117C TYR* 3.3 17.9 - - - +
150C TYR* 3.1 40.4 + - + +
151C THR* 3.4 25.6 + - + +
152C PHE 3.1 1.0 - - - -
153C LEU* 1.3 77.5 - - - +
155C GLN* 1.3 67.5 + - - +
157C CYS 3.7 0.9 - - - -
158C PRO* 3.3 25.7 - - + +
159C ASP* 3.7 9.3 + - - +
166C ARG* 3.3 37.6 + - - +
191C LEU* 5.6 2.4 - - - +
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Residues in contact with GLN 155 (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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30C LEU* 3.8 40.2 - - + +
31C ALA 5.2 0.9 - - - +
32C VAL* 4.7 5.8 - - + -
151C THR* 3.6 17.2 - - - +
152C PHE* 2.8 19.4 + - + +
154C GLN* 1.3 79.7 - - - +
156C LEU* 1.3 61.5 + - - +
158C PRO* 4.9 2.6 - - - +
389C VAL* 2.9 48.4 - - + +
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Residues in contact with LEU 156 (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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30C LEU* 3.6 24.5 - - + -
67C PRO* 4.0 31.0 - - + -
121C PRO 4.8 0.9 - - - +
122C LEU* 4.4 3.1 - - + -
123C PRO* 3.8 34.5 - - + +
125C PHE* 3.9 23.6 - - + -
152C PHE* 3.6 35.2 - - + +
153C LEU* 3.2 14.9 + - + +
155C GLN* 1.3 76.9 - - - +
157C CYS* 1.3 61.4 + - - +
158C PRO* 4.4 2.2 - - - +
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Residues in contact with CYS 157 (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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117C TYR* 2.4 32.8 + - + -
119C ALA* 3.7 11.4 - - - -
120C ALA* 3.7 33.0 - - - -
121C PRO* 3.6 27.1 - - - +
122C LEU* 3.9 13.5 - - + -
153C LEU 2.7 12.1 + - - +
154C GLN 3.5 2.0 - - - -
155C GLN 3.3 1.0 - - - -
156C LEU* 1.3 77.3 - - - +
158C PRO* 1.3 67.4 - - - +
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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