Contacts of the helix formed by residues 112 - 126 (chain L) in PDB entry 6NRB
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 ILE 112 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L SER 3.1 22.7 - - - +
109L VAL 3.2 9.2 - - - +
111L ILE* 1.3 84.8 - - + +
113L ALA* 1.3 64.8 + - - +
114L GLY 3.1 2.7 - - - -
115L SER* 3.0 27.3 + - - +
116L LEU* 3.3 17.8 + - + +
429L GLU* 4.9 9.6 - - + +
454L PHE* 5.5 3.1 - - + -
458L MET* 5.8 4.7 - - + -
461L ILE* 4.6 12.8 - - + -
518L ALA* 3.4 34.8 - - + +
519L LEU* 3.6 28.0 - - + +
522L ALA* 3.9 9.0 - - + +
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Residues in contact with ALA 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L ALA* 4.2 2.0 - - + -
91L LEU* 3.6 37.0 - - + +
94L LEU* 4.1 5.2 - - + -
109L VAL 2.8 14.5 + - - +
110L VAL* 3.2 21.4 + - - +
112L ILE* 1.3 78.8 - - - +
114L GLY* 1.3 55.5 + - - +
116L LEU 4.3 0.3 + - - -
117L LEU* 3.2 24.9 + - - +
522L ALA* 4.2 8.5 - - - -
526L VAL* 3.9 10.9 - - - +
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Residues in contact with GLY 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L LYS* 4.6 8.8 - - - +
45L ALA* 3.6 20.0 - - - +
46L ASP* 4.8 4.7 - - - -
49L ARG* 5.4 3.6 - - - -
111L ILE 4.0 4.1 + - - -
112L ILE 3.1 0.4 - - - -
113L ALA* 1.3 75.5 - - - +
115L SER* 1.3 61.4 + - - +
116L LEU 3.2 2.5 - - - -
117L LEU* 3.5 13.3 - - - +
118L ASP* 2.8 35.0 + - - +
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Residues in contact with SER 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L ARG* 4.1 0.4 + - - +
111L ILE 3.4 5.0 + - - -
112L ILE* 3.0 31.2 + - - +
114L GLY* 1.3 78.2 - - - +
116L LEU* 1.3 57.0 + - - +
118L ASP* 3.1 28.5 - - - +
119L SER 4.0 0.5 + - - -
454L PHE* 3.1 28.2 - - - -
457L ALA* 3.3 15.4 + - - +
458L MET* 5.0 2.1 - - - -
460L VAL* 3.3 22.7 - - - +
461L ILE* 4.2 1.2 - - - +
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Residues in contact with LEU 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L ILE* 3.3 8.3 + - + +
113L ALA 4.6 1.1 - - - +
114L GLY 3.2 0.2 - - - -
115L SER* 1.3 75.4 - - - +
117L LEU* 1.3 64.1 + - - +
118L ASP 3.0 1.8 - - - -
119L SER* 3.0 8.2 + - - -
120L CYS* 3.0 23.3 + - - -
137L PHE* 3.5 34.7 - - + +
454L PHE* 3.4 38.1 - - + -
522L ALA* 3.2 42.4 - - + +
523L THR* 3.6 15.0 - - - +
526L VAL* 3.8 19.1 - - + -
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Residues in contact with LEU 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L ASN 4.1 3.4 - - - +
38L ILE* 3.4 43.0 - - + +
41L ALA* 3.9 15.3 - - + +
42L LYS* 3.1 62.2 + - - +
90L MET* 6.5 0.4 - - + -
91L LEU* 5.1 1.8 - - + -
113L ALA 3.2 20.2 - - - +
114L GLY* 3.2 7.6 + - - +
116L LEU* 1.3 73.3 - - - +
118L ASP* 1.3 66.8 + - - +
120L CYS* 3.4 9.5 + - - +
121L THR 3.7 1.4 + - - -
526L VAL* 3.7 25.4 - - + -
529L ILE* 5.0 5.6 - - + -
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Residues in contact with ASP 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L LYS* 4.4 13.5 + - - +
46L ASP* 5.3 1.9 - - - +
114L GLY 2.8 22.0 + - - +
115L SER* 3.1 24.2 - - - +
117L LEU* 1.3 81.1 - - - +
119L SER* 1.3 62.4 + - - +
121L THR* 3.2 15.4 + - - -
122L LYS* 4.2 11.0 + - - +
453L ALA 5.6 0.2 - - - +
457L ALA* 3.4 24.1 - - + +
460L VAL* 3.8 15.4 - - - +
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Residues in contact with SER 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L LEU 3.0 7.9 + - - -
118L ASP* 1.3 75.6 - - - +
120L CYS* 1.3 66.2 + - - +
121L THR 3.4 0.2 - - - -
122L LYS* 3.3 6.6 + - - +
123L LEU* 2.8 47.8 + - - +
137L PHE* 5.5 4.0 - - - -
450L CYS 4.5 0.4 - - - -
453L ALA* 3.0 18.8 + - - -
454L PHE* 2.8 41.1 + - - +
457L ALA* 4.4 1.4 - - - +
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Residues in contact with CYS 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ILE* 3.6 22.7 - - + -
116L LEU 3.0 25.5 + - - -
117L LEU* 3.5 29.4 - - - +
118L ASP 3.2 0.4 - - - -
119L SER* 1.3 74.9 - - - +
121L THR* 1.3 65.7 + - - +
123L LEU* 3.9 3.3 - - - +
124L LEU* 3.0 32.3 + - + +
133L ILE* 4.5 7.4 - - - +
137L PHE* 3.4 27.1 - - - -
526L VAL* 3.9 3.8 - - - -
529L ILE* 5.8 0.7 - - - -
530L LEU* 5.0 7.2 - - + -
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Residues in contact with THR 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L PHE* 5.6 8.3 - - + +
38L ILE* 3.6 26.7 - - + +
39L SER* 5.8 2.2 - - - +
42L LYS* 3.6 14.9 + - - +
117L LEU 3.7 0.4 + - - -
118L ASP 3.2 13.3 + - - -
120L CYS* 1.3 76.0 - - - +
122L LYS* 1.3 76.7 + - - +
124L LEU* 3.2 8.0 + - - +
125L GLN* 2.9 41.7 + - - +
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Residues in contact with LYS 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E GLN* 3.6 34.6 + - - +
118L ASP 4.3 10.5 - - - +
119L SER* 3.3 8.6 + - - +
121L THR* 1.3 87.1 + - - +
123L LEU* 1.3 55.2 + - + +
125L GLN* 2.8 14.4 + - - +
126L LYS* 2.6 40.7 + - + +
453L ALA* 4.9 15.5 - - + -
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Residues in contact with LEU 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L SER* 2.8 39.9 + - - +
120L CYS 4.0 0.4 - - - +
122L LYS* 1.3 69.8 - - + +
124L LEU* 1.3 64.5 + - - +
126L LYS* 3.1 24.0 + - + -
128L ILE* 3.0 36.2 + - + +
133L ILE* 3.6 34.3 - - + -
136L SER* 4.9 1.6 - - - -
137L PHE* 5.6 2.0 - - + -
449L TYR 4.6 0.2 - - - -
450L CYS* 3.5 52.9 - - + +
453L ALA* 4.5 9.9 - - + -
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Residues in contact with LEU 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L ARG* 3.5 44.2 - - - +
35L PHE* 3.5 27.6 - - + -
38L ILE* 3.6 24.9 - - + -
120L CYS 3.0 17.4 + - - +
121L THR 3.6 4.0 - - - +
123L LEU* 1.3 75.9 - - - +
125L GLN* 1.3 60.6 + - + +
126L LYS 3.6 0.2 + - - -
127L GLY* 4.2 5.2 + - - -
128L ILE 3.9 4.8 + - - +
130L PRO* 3.6 24.5 - - + -
133L ILE* 3.4 14.5 - - + +
530L LEU* 4.5 6.1 - - + -
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Residues in contact with GLN 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L PHE* 5.0 18.6 - - + -
121L THR* 2.9 33.7 + - - +
122L LYS* 2.8 15.4 + - - +
124L LEU* 1.3 78.3 - - + +
126L LYS* 1.3 60.7 + - - +
127L GLY 3.3 2.1 + - - -
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Residues in contact with LYS 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460E MET* 4.1 25.3 - - + +
470E PRO* 4.8 4.2 - - - +
471E ILE* 3.3 39.6 - - + +
474E MET* 4.6 4.4 - - - +
122L LYS* 2.6 19.7 + - + +
123L LEU* 3.1 23.6 + - + +
125L GLN* 1.3 75.9 - - - +
127L GLY* 1.3 58.1 + - - +
128L ILE* 3.6 14.1 - - + -
449L TYR* 3.6 27.5 - - - -
453L ALA* 6.2 0.7 - - + -
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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