Contacts of the helix formed by residues 141 - 157 (chain C) in PDB entry 1GT0
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 GLU 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C LYS* 6.2 1.8 - - - -
135C ALA* 4.1 0.4 - - - -
139C ASN 4.1 2.6 - - - +
140C MET* 1.3 102.8 - - - +
142C LYS* 1.3 69.7 + - - +
143C GLU* 3.3 3.4 - - + +
144C VAL* 3.0 44.0 + - + +
145C ILE* 3.2 9.2 + - - +
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Residues in contact with LYS 142 (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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131C ILE* 4.0 7.9 - - + +
132C THR* 3.5 45.5 - - + +
135C ALA* 3.8 13.4 - - + +
140C MET 3.6 3.4 + - - -
141C GLU* 1.3 67.4 - - - +
143C GLU* 1.3 58.3 + - - +
145C ILE* 2.7 28.6 + - - +
146C ARG* 2.8 23.2 + - - +
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C GLU* 3.3 4.0 - - + +
142C LYS* 1.3 81.6 - - - +
144C VAL* 1.3 59.1 + - + +
146C ARG* 2.5 49.3 + - - +
147C VAL* 2.9 42.7 + - + +
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Residues in contact with VAL 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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18A A 5.8 0.7 - - - -
19A A 4.0 24.0 - - - +
103C LYS* 4.6 15.7 - - + -
106C THR 6.1 0.4 - - - +
108C ILE* 4.1 24.7 - - + -
140C MET* 5.2 3.1 - - - -
141C GLU* 3.0 43.2 + - + +
143C GLU* 1.3 77.8 - - + +
145C ILE* 1.3 65.9 + - + +
147C VAL* 3.3 6.4 + - - +
148C TRP* 2.9 27.5 + - + +
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Residues in contact with ILE 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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108C ILE* 5.9 0.2 - - + -
116C LEU* 3.7 35.7 - - + -
131C ILE* 4.0 19.3 - - + +
134C ILE* 4.4 6.7 - - + -
135C ALA* 3.6 29.2 - - + +
138C LEU* 4.8 3.6 - - + -
140C MET* 3.9 22.2 - - + -
141C GLU 3.8 4.5 - - - +
142C LYS 2.7 11.2 + - - +
144C VAL* 1.3 77.1 - - + +
146C ARG* 1.3 71.1 + - - +
148C TRP* 3.2 10.0 + - + +
149C PHE* 3.2 36.9 + - + -
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Residues in contact with ARG 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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27B C 4.4 17.9 + - - +
28B C 6.1 5.4 - - + -
128C SER* 4.3 24.0 + - - +
131C ILE* 3.9 38.0 - - + +
132C THR* 5.6 1.8 + - - -
142C LYS* 2.8 18.1 + - - +
143C GLU* 2.5 54.4 + - - +
144C VAL 3.2 0.2 - - - -
145C ILE* 1.3 80.8 - - - +
147C VAL* 1.3 66.3 + - + +
148C TRP 3.2 0.3 + - - -
149C PHE* 3.2 11.5 + - - +
150C SER* 3.3 11.7 + - - -
153C ARG* 5.1 1.2 + - - -
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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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18A A 5.2 4.3 - - + -
19A A 3.4 25.8 - - + +
20A T 3.7 22.9 - - + +
143C GLU* 2.9 34.3 + - + +
144C VAL* 3.7 5.8 - - - +
145C ILE 3.2 0.2 - - - -
146C ARG* 1.3 79.0 - - + +
148C TRP* 1.3 57.8 + - - +
150C SER* 3.3 7.6 + - - -
151C ASN* 2.9 45.3 + - - +
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Residues in contact with TRP 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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18A A 3.2 27.4 + - - +
108C ILE* 4.2 13.9 - - + +
113C ARG* 4.0 24.4 - - - +
116C LEU* 3.5 60.6 - - + +
117C GLU* 4.2 12.8 - - - -
120C PHE* 3.9 13.5 - - + -
144C VAL* 2.9 18.3 + - + +
145C ILE* 3.5 9.0 - - + +
146C ARG 3.1 0.2 - - - -
147C VAL* 1.3 77.1 - - - +
149C PHE* 1.3 84.8 + + - +
151C ASN* 4.0 4.4 - - - +
152C ARG* 2.6 64.8 + - + -
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Residues in contact with PHE 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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116C LEU* 3.9 13.0 - - + -
119C SER* 3.8 14.1 - - - -
120C PHE* 4.1 19.5 - + - -
123C ASN 3.7 13.7 - - - -
124C GLN 4.0 6.7 - - - -
126C PRO* 3.4 35.4 - - + -
131C ILE* 5.0 4.9 - - + -
134C ILE* 3.7 26.7 - - + -
145C ILE* 3.2 38.7 + - + -
146C ARG* 3.2 9.2 + - - +
148C TRP* 1.3 98.0 - + - +
150C SER* 1.3 63.3 + - - +
152C ARG* 4.3 0.6 - - - +
153C ARG* 3.0 41.9 + - - +
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Residues in contact with SER 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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20A T 6.2 0.4 - - - -
28B C 5.1 2.5 - - - +
29B C 3.2 35.8 + - - -
30B A 5.6 0.2 + - - -
146C ARG* 3.3 10.0 + - - -
147C VAL* 3.5 11.7 - - - -
148C TRP 3.2 0.4 - - - -
149C PHE* 1.3 80.1 - - - +
151C ASN* 1.3 66.3 + - - +
153C ARG* 3.2 25.3 + - - +
154C GLN* 3.1 25.6 + - - +
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Residues in contact with ASN 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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17A T 5.1 4.3 - - + -
18A A 3.0 37.0 + - + +
19A A 2.9 46.8 + - - +
20A T 5.1 0.7 - - - +
30B A 4.8 2.3 + - - -
147C VAL* 2.9 25.9 + - - +
148C TRP* 4.0 4.8 - - - +
150C SER* 1.3 81.8 - - - +
152C ARG* 1.3 58.2 + - - +
154C GLN* 2.9 26.8 + - - +
155C LYS* 3.0 13.9 + - - +
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Residues in contact with ARG 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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113C ARG* 5.6 3.4 - - - +
117C GLU* 2.3 47.1 + - - -
120C PHE* 3.2 31.8 - - + -
148C TRP* 2.6 55.8 + - + +
149C PHE 4.3 1.1 - - - +
151C ASN* 1.3 74.6 - - - +
153C ARG* 1.3 61.7 + - - +
155C LYS* 4.0 35.6 - - - +
156C GLU* 3.2 27.1 + - - +
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Residues in contact with ARG 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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27B C 5.8 0.2 + - - -
28B C 4.9 14.6 + - - +
29B C 5.0 11.3 + - - -
120C PHE* 4.3 4.0 - - - -
124C GLN* 2.6 60.1 + - + +
125C LYS* 4.2 19.7 - - - +
126C PRO* 4.4 1.6 + - - +
146C ARG 5.1 0.8 + - - -
149C PHE* 3.0 38.7 + - - +
150C SER* 3.2 32.7 + - - +
151C ASN 3.1 0.2 - - - -
152C ARG* 1.3 77.8 - - - +
154C GLN* 1.3 65.4 + - - +
156C GLU* 3.2 18.1 - - + +
157C LYS* 3.4 9.5 + - - +
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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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29B C 3.2 45.1 + - - +
30B A 3.6 22.5 + - + +
31B T 5.0 6.3 + - + +
150C SER* 3.1 16.2 + - - +
151C ASN* 2.9 18.5 + - + +
153C ARG* 1.3 76.1 - - - +
155C LYS* 1.3 56.5 + - - +
156C GLU 2.8 14.7 + - - -
157C LYS* 3.0 19.0 + - - +
158C ARG* 3.7 7.8 + - - +
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Residues in contact with LYS 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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17A T 2.8 38.3 + - - +
113C ARG* 3.9 10.4 - - - +
151C ASN 3.0 8.2 + - - +
152C ARG* 3.5 36.3 + - - +
154C GLN* 1.3 78.8 - - - +
156C GLU* 1.3 59.0 + - - +
158C ARG* 4.0 4.9 - - - +
159C ILE 3.4 18.0 + - - -
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Residues in contact with GLU 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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120C PHE* 4.2 9.3 - - + -
124C GLN* 3.3 30.8 - - - +
152C ARG* 3.2 30.4 + - - +
153C ARG* 3.2 15.5 - - - +
154C GLN 2.8 1.4 + - - -
155C LYS* 1.3 76.9 - - - +
157C LYS* 1.3 54.6 + - - +
158C ARG 2.6 18.1 + - - -
159C ILE 3.8 4.3 + - - -
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Residues in contact with LYS 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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153C ARG 3.4 7.4 + - - +
154C GLN* 3.0 12.1 + - - +
156C GLU* 1.3 76.4 - - - +
158C ARG* 1.3 59.1 + - - +
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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