Contacts of the helix formed by residues 134 - 151 (chain A) in PDB entry 3C2B
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 ARG 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.8 4.3 - - + -
101A VAL* 5.9 4.5 - - + -
102A LEU* 5.1 6.7 - - + -
129A LEU 4.0 4.0 + - - +
130A LEU 5.5 1.2 + - - +
131A GLU 5.5 0.4 - - - -
132A ARG 3.3 0.6 - - - +
133A GLY* 1.3 79.3 - - - +
135A ARG* 1.3 59.6 + - - +
136A GLN 3.3 3.3 + - - -
137A ILE* 3.4 21.6 + - + -
138A ASP* 2.8 62.0 + - - +
163A TYR* 4.0 0.2 + - - -
167A TYR* 3.5 37.7 + - - -
302A FMT 2.4 34.6 + - - -
173B ASP* 2.9 23.4 + - - +
177B ARG* 3.7 15.1 - - - +
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLU* 2.7 33.4 + - - +
132A ARG* 3.7 35.2 + - - +
133A GLY 3.7 1.4 - - - -
134A ARG* 1.3 77.2 - - - +
136A GLN* 1.3 64.5 + - + +
138A ASP* 3.8 7.2 - - - +
139A ARG* 2.9 40.5 + - + +
142A ARG* 5.4 1.0 + - - +
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 5.2 11.9 - - + -
73A ARG 4.4 7.0 - - - +
74A THR* 3.3 29.6 + - - +
75A PHE* 3.9 38.4 + - + +
134A ARG 3.3 0.6 - - - -
135A ARG* 1.3 82.4 - - + +
137A ILE* 1.3 66.9 + - - +
139A ARG* 3.5 9.4 + - - +
140A ARG* 3.0 24.3 + - - +
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 3.5 34.9 - - + -
94A PHE* 3.4 26.0 - - + -
97A ASP* 4.8 0.2 - - + -
98A LEU* 4.0 34.3 - - + +
101A VAL* 4.4 21.5 - - + -
134A ARG* 3.4 26.8 + - + +
136A GLN* 1.3 77.8 - - - +
138A ASP* 1.3 62.7 + - - +
140A ARG* 3.2 6.5 - - - +
141A ALA* 3.1 19.1 + - - +
163A TYR* 3.5 18.2 - - - +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 2.8 56.2 + - - +
135A ARG* 3.8 7.0 + - - +
136A GLN 3.3 0.2 - - - -
137A ILE* 1.3 73.5 - - - +
139A ARG* 1.3 58.3 + - - +
141A ALA* 3.3 2.3 + - - +
142A ARG* 3.1 60.7 + - - +
163A TYR* 2.7 38.7 + - + -
302A FMT 4.5 0.8 - - - +
177B ARG* 4.5 6.1 + - - -
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Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 5.7 6.3 - - - +
135A ARG* 2.9 29.4 + - + +
136A GLN* 4.0 11.9 - - - +
137A ILE 3.3 0.2 - - - -
138A ASP* 1.3 73.4 - - - +
140A ARG* 1.3 65.7 + - - +
142A ARG* 3.9 12.3 - - + +
143A GLY* 2.9 22.2 + - - -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG* 5.8 1.6 - - - +
75A PHE* 3.6 37.8 - - + +
76A GLU* 3.5 37.5 + - - +
77A LYS 5.0 0.2 - - - -
78A ALA* 4.3 12.7 - - - +
90A HIS* 4.4 25.0 + - - -
93A VAL* 5.5 5.3 - - - +
94A PHE* 3.8 25.8 - - + +
97A ASP* 5.4 3.4 + - - -
136A GLN 3.0 13.6 + - - +
137A ILE* 3.2 12.8 - - - +
139A ARG* 1.3 77.3 - - - +
141A ALA* 1.3 62.8 + - - +
143A GLY* 3.6 1.3 - - - -
144A LEU* 3.0 52.8 + - - +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 6.4 0.2 - - - -
94A PHE* 3.4 26.2 - - + -
137A ILE 3.1 4.7 + - - +
138A ASP 3.7 0.9 - - - +
139A ARG 3.3 0.2 - - - -
140A ARG* 1.3 78.0 - - - +
142A ARG* 1.3 57.7 + - - +
144A LEU* 3.3 6.5 + - - +
145A ILE* 2.9 38.2 + - + +
163A TYR* 3.4 42.2 - - + -
166A PHE* 5.5 1.3 - - + -
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ARG* 5.4 1.2 + - - +
138A ASP* 3.1 46.0 + - - +
139A ARG* 4.0 10.5 - - + +
141A ALA* 1.3 71.9 - - - +
143A GLY* 1.3 57.1 + - - +
145A ILE* 3.8 7.5 - - - +
146A GLU* 2.8 37.6 + - - +
159A ALA 6.2 0.2 - - - +
160A GLU* 4.5 23.7 + - + +
163A TYR* 4.2 23.1 - - + -
302A FMT 5.8 0.6 + - - -
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Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 3.5 18.1 - - - +
139A ARG 2.9 15.4 + - - -
140A ARG 3.6 4.0 - - - -
142A ARG* 1.3 77.4 - - - +
144A LEU* 1.3 55.0 + - - +
146A GLU* 3.7 5.2 - - - +
147A ALA* 2.9 29.5 + - - +
150A ARG* 5.1 2.5 + - - -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 3.7 10.0 - - + +
82A VAL* 5.8 1.8 - - + -
87A LEU* 4.0 12.4 - - + +
90A HIS* 3.5 56.3 - - + +
91A LEU* 3.9 20.2 - - + -
94A PHE* 3.9 18.8 - - + -
140A ARG* 3.0 37.5 + - - +
141A ALA* 3.4 10.5 - - - +
143A GLY* 1.3 72.9 - - - +
145A ILE* 1.3 58.7 + - - +
147A ALA* 3.4 7.8 + - + +
148A GLY* 2.9 26.0 + - - -
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 4.9 6.7 - - + -
141A ALA* 2.9 26.4 + - - +
142A ARG* 3.8 5.8 - - - +
144A LEU* 1.3 73.9 - - + +
146A GLU* 1.3 58.7 + - - +
148A GLY 3.4 0.7 + - - -
149A ARG* 2.9 27.5 + - - +
154A LEU* 3.6 12.8 - - + +
156A PHE* 3.5 30.5 - - + -
159A ALA* 4.5 8.7 - - + +
162A ALA* 4.5 6.5 - - + -
163A TYR* 3.7 44.9 - - + +
166A PHE* 4.8 5.8 - - + -
199A PHE* 4.1 22.4 - - + -
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Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG 2.8 19.7 + - - +
143A GLY* 3.7 5.8 - - - +
145A ILE* 1.3 76.7 - - - +
147A ALA* 1.3 56.3 + - - +
149A ARG* 2.6 49.0 + - - +
150A ARG* 2.8 60.1 + - - +
156A PHE* 5.0 3.3 - - - -
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 4.8 3.6 - - + -
79A GLY 3.5 24.7 - - - +
80A ASP 3.9 2.2 - - - +
82A VAL* 4.2 18.2 - - + -
87A LEU* 5.8 0.2 - - + -
143A GLY 2.9 21.1 + - - +
144A LEU* 3.6 9.4 - - + +
146A GLU* 1.3 73.9 - - - +
148A GLY* 1.3 59.1 + - - +
150A ARG* 3.4 16.4 + - - +
151A SER* 2.9 31.4 + - - -
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Residues in contact with GLY 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 4.4 3.0 - - - +
87A LEU* 4.0 20.6 - - - -
144A LEU 2.9 18.4 + - - -
145A ILE 3.7 2.9 - - - -
146A GLU 3.3 0.2 - - - -
147A ALA* 1.3 68.2 - - - +
149A ARG* 1.3 62.5 + - - +
151A SER* 3.4 4.7 + - - -
153A TYR* 2.9 30.7 + - - +
154A LEU* 3.3 17.8 + - - -
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE 2.9 14.2 + - - +
146A GLU* 2.6 41.8 + - - +
148A GLY* 1.3 72.0 - - - +
150A ARG* 1.3 82.4 + - - +
152A GLY* 2.9 16.5 + - - -
154A LEU* 3.6 24.6 - - - +
155A ARG* 5.5 0.9 - - - -
156A PHE* 3.8 31.6 - - + +
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA 5.6 2.0 + - - -
79A GLY 4.2 0.4 + - - -
80A ASP* 2.4 67.1 + - - +
81A ARG* 3.9 18.6 + - + -
143A GLY* 5.1 2.0 + - - -
146A GLU* 2.8 57.2 + - - +
147A ALA* 3.4 23.8 - - - +
148A GLY 3.5 0.2 - - - -
149A ARG* 1.3 85.3 - - - +
151A SER* 1.3 57.5 + - - +
152A GLY* 3.1 3.3 + - - -
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Residues in contact with SER 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 3.6 23.9 + - - +
82A VAL* 3.2 25.2 + - - -
147A ALA 2.9 17.6 + - - -
148A GLY 3.4 0.9 + - - -
149A ARG 3.0 1.2 - - - -
150A ARG* 1.3 76.8 - - - +
152A GLY* 1.3 56.5 + - - +
153A TYR* 3.3 31.4 + - - -
207A LYS* 2.8 30.5 + - - -
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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
------------------------------------------------------------
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