Contacts of the strand formed by residues 127 - 135 (chain B) in PDB entry 6CNC
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 ALA 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 5.0 5.1 - - + +
101B GLY* 4.7 11.2 - - - +
109B LYS* 6.0 0.2 - - + -
112B LEU* 4.1 12.1 - - + -
126B SER* 1.3 77.5 + - - +
128B PRO* 1.3 74.3 - - + +
129B ILE* 5.0 0.2 - - - +
152B MET* 2.9 31.9 + - - +
154B ILE* 3.7 33.1 - - + +
160B LYS* 5.5 2.2 - - + -
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Residues in contact with PRO 128 (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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100B VAL* 3.7 2.8 - - - -
101B GLY* 3.1 27.2 + - - -
109B LYS* 3.9 21.3 - - + -
111B TYR 5.3 1.8 - - - +
112B LEU* 5.5 0.7 - - + -
126B SER 4.6 1.6 - - - +
127B ALA* 1.3 89.3 - - + +
129B ILE* 1.3 66.9 + - - +
130B TYR* 3.9 28.3 - - + +
148B GLU* 4.5 7.4 - - + -
150B GLY 3.6 6.7 - - - +
151B ARG* 3.6 22.2 - - + -
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 5.2 6.1 - - + -
98B ILE* 4.8 9.2 - - + -
99B ARG 3.8 2.9 - - - +
100B VAL* 3.5 19.5 - - + -
128B PRO* 1.3 71.7 - - - +
130B TYR* 1.3 83.3 + - - +
131B VAL* 4.3 4.0 - - + -
147B VAL 4.4 0.2 - - - -
148B GLU* 3.3 18.8 - - - +
149B ILE* 3.5 33.0 - - + -
150B GLY 2.6 24.9 + - - +
151B ARG 4.3 0.7 - - - +
152B MET* 3.4 38.8 - - + +
388B PHE* 5.2 15.3 - - + -
429B ILE* 5.8 1.6 - - + -
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 3.6 2.3 - - - -
99B ARG* 2.8 39.3 + - + +
101B GLY* 4.0 11.7 - - - -
102B LYS 3.3 35.2 - - - +
103B LYS* 3.5 39.9 + - + +
109B LYS* 3.5 21.8 + - - -
128B PRO* 3.9 12.0 - - + +
129B ILE* 1.3 83.0 - - - +
131B VAL* 1.3 68.1 + - - +
146B ASP* 3.3 20.4 - - - +
147B VAL 3.3 3.4 - - - -
148B GLU* 3.2 40.9 + - + -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TYR* 5.2 8.3 - - + -
97B ASP 3.4 9.6 - - - +
98B ILE* 3.5 20.2 - - + -
99B ARG* 6.4 0.2 - - - -
129B ILE* 4.3 1.3 - - + -
130B TYR* 1.3 79.7 - - - +
132B ASP* 1.3 76.5 + - - +
133B ILE* 3.5 25.6 - - + -
146B ASP* 2.9 10.2 - - - +
147B VAL* 2.8 34.6 + - + +
149B ILE* 3.6 38.6 - - + -
392B PHE* 6.3 2.5 - - + -
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Residues in contact with ASP 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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95B TYR* 3.6 1.6 - - - +
96B VAL* 2.9 45.5 + - + +
97B ASP* 3.3 23.4 + - - +
99B ARG* 3.7 16.1 + - - -
131B VAL* 1.3 90.5 - - - +
133B ILE* 1.3 65.8 + - - +
144B HIS* 5.7 4.5 - - + +
145B LYS 2.6 21.9 - - - +
146B ASP* 3.1 15.3 - - - +
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Residues in contact with ILE 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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93B LEU* 3.4 29.4 - - + -
94B LYS 3.0 24.5 - - - +
95B TYR* 3.5 27.4 - - + +
131B VAL* 3.5 29.6 - - + -
132B ASP* 1.3 78.1 - - - +
134B GLU* 1.3 72.6 + - - +
135B TYR* 3.2 13.2 - - + -
144B HIS* 2.9 20.3 - - - +
145B LYS 4.0 6.5 + - - +
147B VAL* 4.8 12.1 - - + -
149B ILE* 5.7 1.1 - - + -
419B LEU* 5.6 8.0 - - + +
422B ILE* 6.5 1.6 - - + -
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Residues in contact with GLU 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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92B TYR* 4.4 9.6 + - + +
94B LYS* 2.5 67.0 + - + +
96B VAL* 4.6 14.7 - - + +
132B ASP 4.2 0.8 - - - -
133B ILE* 1.3 69.0 - - - +
135B TYR* 1.3 54.9 + - - +
142B ILE* 5.3 3.8 - - + +
143B MET 3.8 1.1 - - - +
144B HIS* 3.6 30.8 + - + -
396S LYS* 3.3 27.4 + - - +
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Residues in contact with TYR 135 (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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91B PHE* 5.7 1.8 - + + -
92B TYR* 3.2 10.5 - - - +
93B LEU* 3.5 25.4 - - + -
133B ILE* 3.2 15.5 - - + -
134B GLU* 1.3 73.6 - - - +
136B THR* 1.3 88.4 + - - +
137B ARG* 3.6 34.4 + - + -
142B ILE* 3.0 26.5 - - - +
143B MET* 3.1 60.2 + - + -
144B HIS* 3.7 7.9 - - - -
145B LYS* 3.4 9.0 + - - -
417B ASP* 4.2 3.9 - - + +
419B LEU* 3.4 42.2 - - + +
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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