Contacts of the helix formed by residues 121 - 137 (chain R) in PDB entry 6CNB
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 121 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119R GLY 4.7 5.3 + - - -
120R ARG* 1.3 78.2 - - - +
122R SER* 1.3 66.6 + - - +
123R GLN* 3.1 11.9 + - + +
124R ASN* 3.1 35.2 + - - +
125R VAL* 3.2 11.8 + - - +
23X C 2.9 36.3 + - - -
24X T 3.0 53.9 + - - -
25X T 3.4 3.1 - - - -
47Y G 5.7 0.4 - - - +
49Y A 5.4 8.7 + - - -
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Residues in contact with SER 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120R ARG 3.3 1.3 + - - -
121R ARG* 1.3 70.8 - - - +
123R GLN* 1.3 73.7 + - - +
125R VAL* 3.2 9.2 + - - +
126R ILE* 3.1 28.1 + - - +
25X T 2.4 57.6 + - - -
26X T 4.5 4.0 + - - -
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Residues in contact with GLN 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R ARG* 4.0 10.9 - - - +
122R SER* 1.3 85.6 + - - +
124R ASN* 1.3 70.1 + - - +
126R ILE* 3.2 11.3 - - + +
127R ALA* 2.9 26.1 + - - +
150R LEU* 3.5 38.1 - - + +
151R GLN* 5.1 7.2 + - - +
157R ILE* 5.9 0.4 - - - -
25X T 4.6 8.2 + - - -
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Residues in contact with ASN 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120R ARG* 5.8 1.3 - - + -
121R ARG* 3.1 31.8 + - + +
123R GLN* 1.3 80.2 - - - +
125R VAL* 1.3 66.3 + - + +
127R ALA* 3.4 6.9 - - - +
128R SER* 3.2 20.4 + - - -
150R LEU* 5.9 1.4 - - - +
152R VAL* 4.1 6.1 - - - +
156R SER* 3.0 16.7 - - - -
157R ILE* 2.9 40.7 + - - +
160R THR* 3.2 27.7 - - + +
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Residues in contact with VAL 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108R TYR* 4.2 11.9 - - + -
116R PHE* 5.1 6.5 - - + +
117R VAL* 3.7 46.2 - - + +
120R ARG* 4.1 22.0 - - + -
121R ARG 3.2 14.3 + - - +
122R SER* 3.5 9.9 - - - +
123R GLN 3.0 1.6 + - - -
124R ASN* 1.3 75.9 - - - +
126R ILE* 1.3 58.9 + - + +
128R SER* 2.9 21.2 + - - -
129R CYS* 2.9 25.9 + - - -
160R THR* 4.2 11.0 - - + -
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Residues in contact with ILE 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R ALA* 5.3 3.1 - - + -
86R LYS* 5.1 14.6 - - + +
87R LEU* 3.4 30.8 - - + +
90R VAL* 4.2 26.7 - - + -
108R TYR* 4.3 21.1 - - + -
122R SER* 3.4 14.1 - - - +
123R GLN* 3.2 17.9 - - + +
125R VAL* 1.3 71.3 - - + +
127R ALA* 1.3 63.5 + - + +
129R CYS* 3.4 10.5 - - - +
130R LEU* 2.8 34.7 + - - +
146R PHE* 5.2 1.8 - - + -
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Residues in contact with ALA 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123R GLN 2.9 19.4 + - - +
124R ASN* 3.4 10.5 - - - +
126R ILE* 1.3 77.5 - - + +
128R SER* 1.3 65.8 + - - +
130R LEU* 2.8 16.1 + - - +
131R TYR* 2.8 12.3 + - - +
146R PHE* 3.3 34.8 - - + -
157R ILE* 4.3 17.7 - - + -
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Residues in contact with SER 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116R PHE* 5.4 0.3 - - - -
124R ASN 3.2 7.6 + - - -
125R VAL* 2.9 18.4 + - - -
127R ALA* 1.3 78.9 - - - +
129R CYS* 1.3 57.2 + - - +
131R TYR* 3.1 9.6 + - - -
132R VAL* 2.7 37.4 + - - +
157R ILE* 5.1 4.5 - - - +
160R THR* 3.8 7.7 - - - +
161R PHE* 3.6 38.4 - - - -
164R MET* 3.2 19.3 - - - -
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Residues in contact with CYS 129 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R LEU* 5.3 3.6 - - + -
104R ALA* 3.3 21.6 - - - +
107R TRP* 4.6 1.9 - - - +
108R TYR* 4.1 36.8 - - + +
111R ALA* 4.4 10.1 - - - -
116R PHE* 6.5 0.7 - - - -
125R VAL* 2.9 40.9 + - - +
126R ILE* 3.4 13.7 - - - +
127R ALA 3.1 0.2 + - - -
128R SER* 1.3 79.7 + - - +
130R LEU* 1.3 58.1 + - - +
132R VAL* 3.2 21.7 - - - +
133R ALA 3.8 0.5 + - - -
164R MET* 4.7 8.5 - - - -
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Residues in contact with LEU 130 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R LEU* 5.4 4.2 - - + +
90R VAL* 3.9 24.2 - - + +
91R SER* 4.6 4.7 - - - -
94R LEU* 5.2 1.8 - - + -
96R ILE* 3.8 33.7 - - + -
100R ILE* 4.7 9.9 - - + -
101R THR* 4.8 8.3 - - + +
104R ALA* 3.8 19.3 - - + -
126R ILE 2.8 16.9 + - - +
127R ALA 2.8 8.8 + - - +
129R CYS* 1.3 71.3 - - - +
131R TYR* 1.3 64.7 + - - +
133R ALA* 3.0 7.1 + - - +
134R CYS* 3.0 25.4 + - + +
146R PHE* 3.5 26.0 - - + -
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Residues in contact with TYR 131 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127R ALA 2.8 18.5 + - - +
128R SER* 3.7 7.0 - - - +
130R LEU* 1.3 73.2 - - - +
132R VAL* 1.3 62.7 + - - +
134R CYS* 3.1 15.4 - - - -
135R ARG* 2.3 78.1 + - + +
141R HIS* 4.1 9.2 - - + -
142R MET* 5.0 7.4 - - - +
143R LEU* 3.6 59.6 + - + +
146R PHE* 4.7 12.3 - + + -
161R PHE* 3.4 40.2 - + - -
176R ALA* 5.8 0.2 - - - +
513R PRO* 4.0 6.5 - - + +
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Residues in contact with VAL 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107R TRP* 4.6 22.7 - - + -
128R SER 2.7 26.5 + - - +
129R CYS* 3.2 16.8 - - - +
131R TYR* 1.3 73.3 - - - +
133R ALA* 1.3 66.4 + - - +
135R ARG* 3.5 5.8 + - - +
136R LYS* 3.0 22.1 + - - +
161R PHE* 3.5 30.3 - - + -
164R MET* 4.1 27.1 - - + -
170R ILE* 4.8 15.3 - - + -
174R PRO* 5.7 0.4 - - - +
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Residues in contact with ALA 133 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B HIS* 5.1 2.6 - - + -
100R ILE* 3.7 18.2 - - + -
103R ALA* 4.8 3.6 - - + -
104R ALA* 3.6 34.8 - - + +
107R TRP* 4.8 9.0 - - + +
129R CYS 4.0 0.2 - - - +
130R LEU 3.0 10.4 + - - +
132R VAL* 1.3 81.6 - - - +
134R CYS* 1.3 56.0 + - - +
136R LYS* 2.5 32.7 + - - +
137R GLU* 3.2 10.0 + - - +
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Residues in contact with CYS 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96R ILE* 5.6 7.4 - - + -
100R ILE* 4.4 15.7 - - + -
130R LEU* 3.0 16.9 + - + +
131R TYR* 3.1 41.1 - - - -
133R ALA* 1.3 76.1 - - - +
135R ARG* 1.3 61.8 + - - +
137R GLU* 3.8 4.4 + - - +
138R LYS 3.6 2.3 + - - -
139R THR* 2.7 43.6 + - - +
141R HIS* 4.6 22.7 - - - +
146R PHE* 5.6 4.3 - - - -
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Residues in contact with ARG 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131R TYR* 2.3 80.6 + - + +
132R VAL* 3.6 7.2 - - - +
134R CYS* 1.3 75.0 - - - +
136R LYS* 1.3 56.9 + - - +
137R GLU 3.0 2.5 - - - -
138R LYS* 2.7 38.8 + - - +
139R THR 5.1 4.7 - - - +
141R HIS 5.0 5.6 - - - -
161R PHE* 4.7 0.8 - - + -
174R PRO* 2.7 56.9 + - + +
175R LEU 4.8 1.0 - - - +
176R ALA* 3.3 28.1 - - - +
513R PRO* 3.1 31.0 - - - +
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Residues in contact with LYS 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B ASN 4.8 1.6 + - - -
801B HIS* 2.9 50.8 + - + +
856B ASN 5.6 5.6 - - - -
857B PRO* 6.2 1.1 - - - -
859B ASN* 5.9 2.6 - - - +
107R TRP* 3.9 25.1 - - + +
132R VAL 3.0 12.4 + - - +
133R ALA* 2.5 19.8 + - - +
135R ARG* 1.3 71.4 - - - +
137R GLU* 1.3 58.4 + - - +
138R LYS* 3.6 8.2 + - - +
173R LEU* 3.4 51.8 - - + +
174R PRO* 5.4 0.2 - - - +
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Residues in contact with GLU 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B ARG* 2.8 29.5 + - - +
801B HIS* 2.3 49.2 + - + +
803B GLN* 5.5 1.4 + - - -
99R TYR* 3.8 5.4 + - - -
100R ILE* 4.1 23.8 - - + -
133R ALA 3.2 6.5 + - - +
134R CYS 4.1 2.0 - - - +
135R ARG 3.0 0.8 - - - -
136R LYS* 1.3 78.3 - - - +
138R LYS* 1.3 70.8 + - - +
139R THR* 3.6 21.3 - - + +
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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