Contacts of the helix formed by residues 105 - 117 (chain L) in PDB entry 6XAV
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 ASP 105 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104L SER* 1.3 78.5 - - - +
106L LYS* 1.3 64.8 + - - +
107L GLU 3.5 0.2 - - - -
108L VAL* 4.0 7.1 + - - +
109L ASP* 3.4 18.9 - - - +
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Residues in contact with LYS 106 (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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289J ASP* 4.8 3.4 + - - -
104L SER* 4.9 5.4 - - - -
105L ASP* 1.3 79.0 - - + +
107L GLU* 1.3 102.1 + - + +
108L VAL 3.2 0.7 - - - -
109L ASP* 3.1 14.4 + - - +
110L ALA* 2.9 26.1 + - + +
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Residues in contact with GLU 107 (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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288J PRO* 3.2 22.0 - - + +
289J ASP* 2.9 52.6 + - - +
290J ILE 3.9 1.6 + - - -
103L ILE* 3.6 12.4 - - + +
104L SER* 3.1 27.2 + - - +
105L ASP 3.5 0.4 - - - -
106L LYS* 1.3 103.3 + - - +
108L VAL* 1.3 60.9 + - - +
110L ALA* 3.0 9.7 + - + +
111L ILE* 2.9 31.7 + - - +
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Residues in contact with VAL 108 (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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9L TRP* 3.5 48.9 - - + +
70L LEU* 5.7 0.4 - - + -
103L ILE* 3.8 25.1 - - + -
104L SER 3.3 22.7 - - - +
105L ASP 4.0 7.8 + - - +
106L LYS 3.2 0.4 - - - -
107L GLU* 1.3 77.6 - - - +
109L ASP* 1.3 61.3 + - - +
111L ILE* 3.3 10.9 - - + +
112L MET* 3.0 28.4 + - + +
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Residues in contact with ASP 109 (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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105L ASP 3.4 17.5 - - - +
106L LYS* 3.1 11.2 + - - +
108L VAL* 1.3 80.2 - - - +
110L ALA* 1.3 60.8 + - - +
112L MET* 3.7 7.1 - - - +
113L ASN* 3.0 28.4 + - - +
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Residues in contact with ALA 110 (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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286J ALA 5.2 0.9 - - - +
288J PRO* 6.3 0.2 - - + -
106L LYS* 2.9 15.4 + - + +
107L GLU* 3.0 15.7 + - + +
109L ASP* 1.3 78.3 - - - +
111L ILE* 1.3 61.5 + - - +
113L ASN* 3.4 6.1 + - - +
114L ARG* 3.2 50.3 + - - +
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Residues in contact with ILE 111 (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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285J LEU* 5.1 0.4 - - + -
288J PRO* 4.3 9.9 - - + -
43L MET* 4.2 18.6 - - + -
45L PRO* 4.8 2.7 - - + -
64L PHE* 4.0 26.2 - - + -
65L PHE* 3.9 31.4 - - + -
70L LEU* 5.1 9.6 - - + -
103L ILE* 5.1 4.5 - - + -
107L GLU 2.9 15.5 + - - +
108L VAL* 3.3 20.0 - - + +
110L ALA* 1.3 73.9 - - - +
112L MET* 1.3 63.0 + - - +
114L ARG* 3.4 23.7 - - + +
115L LEU* 2.8 29.0 + - - +
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Residues in contact with MET 112 (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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22B GLY 4.9 8.5 - - - +
23B LEU* 5.9 0.2 - - + -
41B GLN* 5.7 4.0 - - - +
44B LYS* 6.0 2.5 - - - +
9L TRP* 6.5 1.1 - - - -
43L MET* 6.1 0.2 - - - -
108L VAL* 3.0 21.2 + - + +
109L ASP* 3.7 9.0 - - - +
110L ALA 3.2 0.2 - - - -
111L ILE* 1.3 79.0 - - - +
113L ASN* 1.3 62.5 + - - +
115L LEU* 3.3 17.8 + - - +
116L GLN* 3.2 52.3 + - + +
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Residues in contact with ASN 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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109L ASP 3.0 17.4 + - - +
110L ALA* 3.7 6.3 - - - +
111L ILE 3.3 0.2 - - - -
112L MET* 1.3 76.8 - - - +
114L ARG* 1.3 58.6 + - + +
116L GLN* 3.3 6.3 + - - +
117L GLN* 2.9 37.2 + - - +
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Residues in contact with ARG 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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285J LEU* 3.2 41.6 + - + +
286J ALA* 3.0 30.5 + - - +
287J ALA* 3.7 1.2 - - - +
288J PRO* 3.4 25.9 - - - +
64L PHE* 4.8 12.2 - - + -
110L ALA* 3.2 37.2 + - - +
111L ILE* 3.4 27.2 - - + +
113L ASN* 1.3 76.1 - - + +
115L LEU* 1.3 65.0 + - - +
117L GLN* 3.5 21.9 - - - +
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Residues in contact with LEU 115 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LYS* 6.1 2.5 - - - +
44B LYS* 5.2 9.4 - - - +
43L MET* 3.7 33.4 - - + -
44L VAL 3.5 24.2 - - - +
45L PRO* 3.7 15.9 - - + -
46L THR* 4.8 6.5 - - + +
64L PHE* 5.3 5.8 - - + -
111L ILE* 2.8 20.7 + - + +
112L MET* 3.4 26.2 - - + +
114L ARG* 1.3 79.0 - - - +
116L GLN* 1.3 70.2 + - - +
117L GLN 4.6 0.7 - - - +
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Residues in contact with GLN 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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22B GLY 4.8 1.3 - - - +
23B LEU* 3.4 36.4 - - - +
24B GLU* 2.8 49.5 + - + +
37B ALA* 6.0 1.0 - - - +
41B GLN* 5.3 1.4 + - - -
44B LYS* 5.4 4.9 - - - +
112L MET* 3.2 44.8 + - + +
113L ASN* 3.3 6.3 + - - +
115L LEU* 1.3 92.8 - - - +
117L GLN* 1.3 64.2 + - + +
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Residues in contact with GLN 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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87A ARG* 5.3 10.6 + - - +
88A ARG* 5.4 15.2 + - - +
24B GLU* 3.6 29.1 + - + +
25B ASN* 5.7 4.7 - - - +
28B ARG* 4.6 20.8 - - - +
113L ASN* 2.9 27.1 + - - +
114L ARG* 3.5 19.6 - - - +
115L LEU 4.6 0.7 - - - +
116L GLN* 1.3 81.2 - - + +
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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