Contacts of the helix formed by residues 120 - 134 (chain B) in PDB entry 6R7Y
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 THR 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LYS* 5.1 4.3 - - - +
117B ASP 4.9 6.5 - - - +
118B PHE 3.5 7.8 + - - +
119B LEU* 1.3 77.8 - - - +
121B MET* 1.3 60.5 + - - +
122B ALA* 3.9 3.1 + - - +
123B GLU* 3.0 31.5 + - - +
124B CYS* 3.0 26.5 + - - -
201B ARG* 5.9 5.1 + - - +
202B GLY* 4.1 22.9 + - - +
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO 4.5 7.2 - - - +
18B LEU* 3.8 26.7 - - + -
120B THR* 1.3 75.5 - - - +
122B ALA* 1.3 58.0 + - - +
124B CYS* 3.9 6.2 - - + +
125B GLN* 3.0 59.9 + - - +
173B LEU* 4.4 7.2 - - + +
174B HIS 5.3 0.4 - - - +
175B ASP* 3.9 36.3 - - + +
202B GLY 4.9 0.6 + - - -
203B TYR* 5.5 1.8 - - + -
543B ARG* 3.9 13.9 - - - +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 3.2 3.5 + - - +
121B MET* 1.3 77.3 - - - +
123B GLU* 1.3 61.3 + - + +
125B GLN* 3.4 8.6 + - - +
126B PHE* 2.9 28.6 + - - +
201B ARG 4.7 1.3 - - - +
202B GLY* 3.6 23.4 + - - +
203B TYR 4.0 13.9 - - - +
205B GLY* 4.2 15.7 - - - +
543B ARG* 4.2 3.2 - - - +
546B SER* 3.9 16.6 - - - +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.8 41.2 - - + +
89B VAL 5.3 1.4 + - - +
90B LYS* 3.6 27.6 + - - +
119B LEU* 4.2 5.4 - - + -
120B THR* 3.0 33.7 + - - +
122B ALA* 1.3 77.8 - - + +
124B CYS* 1.3 60.5 + - - +
126B PHE* 3.6 8.4 - - + +
127B ILE* 2.9 35.7 + - + +
201B ARG* 3.5 24.3 + - - +
206B GLU* 5.1 2.9 - - - +
546B SER* 5.7 1.3 - - - +
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Residues in contact with CYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 4.1 17.7 - - + -
79B MET* 3.5 34.3 - - + +
119B LEU* 3.7 30.5 - - - -
120B THR 3.0 26.5 + - - +
121B MET* 3.9 8.3 - - + +
122B ALA 3.3 0.2 - - - -
123B GLU* 1.3 77.7 - - - +
125B GLN* 1.3 62.0 + - - +
127B ILE* 3.4 1.3 + - - -
128B ILE* 3.2 22.5 + - - +
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.6 33.8 + - + +
19B VAL* 4.4 5.8 - - + +
121B MET* 3.0 46.8 + - + +
122B ALA* 3.9 4.7 - - - +
124B CYS* 1.3 75.5 - - - +
126B PHE* 1.3 62.9 + - - +
128B ILE* 3.6 1.9 + - - +
129B LYS* 3.2 17.8 + - - +
172B PRO* 3.7 22.1 - - + +
173B LEU* 3.0 26.1 + - - +
543B ARG* 3.6 22.0 + - - -
545B PHE* 3.5 17.2 - - + -
546B SER 6.1 0.7 - - - +
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Residues in contact with PHE 126 (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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86B VAL* 3.6 34.1 - - + -
88B LEU* 4.7 13.5 - - + -
122B ALA 2.9 18.3 + - - +
123B GLU* 3.6 9.2 - - + +
124B CYS 3.3 0.2 - - - -
125B GLN* 1.3 77.6 - - - +
127B ILE* 1.3 58.3 + - + +
129B LYS* 3.5 6.1 + - + +
130B HIS* 3.0 36.2 + + + +
277B MET* 5.5 2.9 - - + -
545B PHE* 4.9 5.6 - - + -
546B SER* 3.3 34.0 - - - +
547B GLU* 5.1 2.0 - - + -
548B PRO* 3.7 31.9 - - + -
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Residues in contact with ILE 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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78B ARG* 5.4 0.7 - - - +
79B MET* 3.9 23.1 - - + +
82B GLY* 3.8 26.0 - - - +
83B ALA* 3.8 29.4 - - + +
86B VAL* 4.0 20.6 - - + -
88B LEU* 4.0 15.0 - - + -
119B LEU* 4.4 7.4 - - + -
123B GLU 2.9 23.2 + - - +
124B CYS 3.4 3.8 + - - +
125B GLN 3.3 0.2 - - - -
126B PHE* 1.3 77.4 - - + +
128B ILE* 1.3 59.5 + - + +
130B HIS* 3.1 7.3 + - - +
131B GLU* 2.8 36.9 + - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.8 31.2 - - + -
19B VAL* 3.8 24.7 - - + -
50B LEU* 4.6 12.3 - - + +
72B VAL* 3.9 23.1 - - + +
73B GLY* 3.8 27.1 - - - -
74B ALA* 4.1 2.5 - - + +
79B MET* 3.9 17.0 - - + -
124B CYS 3.2 13.6 + - - +
125B GLN 4.2 2.7 - - - +
126B PHE 3.4 0.2 - - - -
127B ILE* 1.3 76.7 - - + +
129B LYS* 1.3 62.5 + - - +
131B GLU* 3.3 7.0 + - + +
132B LEU* 3.1 27.4 + - + +
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 4.9 0.9 - - - +
125B GLN 3.2 17.8 + - - +
126B PHE* 4.0 6.1 - - + +
128B ILE* 1.3 76.9 - - - +
130B HIS* 1.3 58.4 + - - +
132B LEU* 3.4 4.1 + - + -
133B GLU* 3.0 32.2 + - + +
158B LEU* 4.0 26.0 - - + -
162B LEU* 5.9 4.3 - - - +
170B VAL* 4.1 16.7 + - + +
545B PHE* 3.7 48.3 - - + -
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Residues in contact with HIS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 4.9 6.5 + - + +
86B VAL* 3.6 35.1 - - + +
126B PHE* 3.0 30.7 + - + +
127B ILE 3.1 5.1 + - - +
129B LYS* 1.3 78.7 - - - +
131B GLU* 1.3 68.4 + - - +
133B GLU* 3.4 6.5 + - - +
134B ASN* 3.1 51.3 + - - +
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 3.3 24.4 + - - -
48B ALA* 4.8 6.7 - - + +
50B LEU* 4.5 19.1 - - + -
78B ARG* 3.3 26.3 + - - +
82B GLY* 3.9 17.5 - - - +
85B ALA* 4.1 14.4 - - - +
127B ILE* 2.8 27.3 + - + +
128B ILE* 3.3 6.2 + - + +
130B HIS* 1.3 85.8 - - - +
132B LEU* 1.3 65.9 + - - +
134B ASN* 3.5 25.1 - - - +
135B LEU* 3.9 7.6 + - - +
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Residues in contact with LEU 132 (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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19B VAL* 4.7 13.9 - - + -
21B ILE* 4.0 26.9 - - + -
35B LEU* 6.4 0.2 - - + -
39B ILE* 4.3 20.9 - - + -
48B ALA* 5.4 0.7 - - + -
50B LEU* 4.4 15.9 - - + -
72B VAL* 4.9 4.7 - - + -
128B ILE* 3.1 24.2 + - + +
129B LYS* 3.9 6.3 - - - +
131B GLU* 1.3 75.6 - - - +
133B GLU* 1.3 65.5 + - - +
135B LEU* 3.5 33.4 - - + +
156B SER* 4.5 0.7 + - - -
158B LEU* 3.7 40.2 + - + +
170B VAL* 5.2 4.5 - - + -
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Residues in contact with GLU 133 (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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129B LYS* 3.0 23.7 + - + +
130B HIS* 3.7 9.9 - - - +
131B GLU 3.3 0.2 - - - -
132B LEU* 1.3 77.5 - - - +
134B ASN* 1.3 63.7 + - - +
135B LEU 3.0 6.3 + - - -
136B ARG* 5.2 1.6 - - - +
156B SER* 3.3 27.3 + - - -
158B LEU* 4.9 5.3 - - - +
159B ARG* 5.1 13.8 + - - +
283B GLU* 5.0 6.1 - - - +
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Residues in contact with ASN 134 (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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636A LYS* 4.5 16.6 - - - +
43B LYS* 5.5 4.3 - - - -
130B HIS* 3.1 42.8 + - + +
131B GLU* 3.5 18.1 - - - +
132B LEU 3.4 0.2 - - - -
133B GLU* 1.3 76.7 - - - +
135B LEU* 1.3 61.0 + - - +
136B ARG* 3.9 28.7 + - - +
283B GLU* 4.6 6.4 - - - +
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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