Contacts of the helix formed by residues 75 - 87 (chain A) 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 SER 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN* 5.8 1.4 + - - -
51A LEU* 3.8 16.1 - - - +
74A ALA* 1.3 76.4 - - - +
76A LYS* 1.3 63.5 + - - +
77A ILE* 3.4 4.6 + - - +
78A ARG* 3.2 16.8 + - - +
79A MET* 3.0 30.8 + - - +
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER* 1.3 77.4 - - - +
77A ILE* 1.3 67.3 + - + +
79A MET* 3.3 7.9 + - + +
80A LEU* 3.1 33.1 + - + +
113A ASP 4.0 8.0 + - - -
114A ASN* 3.7 12.7 - - - +
115A ASN 3.5 40.8 - - - +
116A ASP* 3.8 17.6 - - + +
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER* 3.4 5.0 - - - +
76A LYS* 1.3 80.0 - - + +
78A ARG* 1.3 56.8 + - - +
80A LEU* 3.4 10.3 + - + +
81A LEU* 3.0 41.9 + - + +
102A TYR* 3.7 31.4 - - + +
105A ARG* 5.8 2.0 - - - +
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 3.3 23.2 - - - +
48A ALA 3.4 22.8 + - - -
49A GLN* 3.4 40.7 + - - +
50A LEU* 4.4 4.4 - - + +
74A ALA* 3.8 15.7 - - + -
75A SER* 3.2 25.0 + - - +
77A ILE* 1.3 78.5 - - - +
79A MET* 1.3 56.8 + - - +
81A LEU* 3.4 16.8 + - - +
82A GLY* 2.9 28.3 + - - +
127A ILE* 5.4 0.6 - - - +
131A GLU* 3.3 37.3 + - - +
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Residues in contact with MET 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 5.1 2.9 - - + -
50A LEU* 5.7 0.7 - - - -
74A ALA* 3.6 27.4 - - + +
75A SER 3.0 16.1 + - - +
76A LYS* 3.3 8.0 + - - +
78A ARG* 1.3 75.5 - - - +
80A LEU* 1.3 61.5 + - + +
82A GLY* 3.4 2.2 + - - +
83A ALA* 2.8 28.8 + - - +
119A LEU* 3.8 17.1 - - + +
124A CYS* 3.5 50.0 - - + +
127A ILE* 3.9 20.1 - - + +
128A ILE* 3.9 17.9 - - + -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LYS* 3.1 21.6 + - + +
77A ILE* 3.8 7.9 - - + +
78A ARG 3.3 0.2 - - - -
79A MET* 1.3 74.7 - - - +
81A LEU* 1.3 60.5 + - - +
83A ALA* 3.2 4.6 + - - +
84A GLU* 3.0 23.7 + - - +
100A PHE* 3.8 26.5 - - + -
102A TYR* 3.7 37.0 - - + +
105A ARG* 4.7 2.7 - - - +
111A PHE* 4.3 23.6 - - + -
118A PHE* 4.5 9.2 - - + -
119A LEU* 4.0 25.4 - - + -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 5.8 1.0 + - - -
49A GLN* 6.0 4.0 - - - +
77A ILE* 3.0 34.5 + - + +
78A ARG* 3.7 19.3 - - - +
80A LEU* 1.3 76.1 - - - +
82A GLY* 1.3 62.3 + - - +
84A GLU* 3.3 9.4 + - + +
85A ALA* 3.2 18.7 + - - +
102A TYR* 4.2 29.2 - - + -
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Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 5.9 0.2 - - - -
78A ARG* 2.9 25.7 + - - +
79A MET 3.6 3.1 - - - -
81A LEU* 1.3 75.8 - - - +
83A ALA* 1.3 58.2 + - - +
85A ALA* 3.1 4.8 + - - +
86A VAL* 3.0 31.9 + - - +
127A ILE* 3.8 18.8 - - - -
131A GLU* 3.9 10.7 - - - +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A MET 2.8 17.5 + - - +
80A LEU* 3.2 8.0 + - - +
82A GLY* 1.3 73.7 - - - +
84A GLU* 1.3 64.1 + - - +
86A VAL 4.5 0.7 - - - +
87A GLY* 3.2 18.4 + - - -
88A LEU* 3.6 23.5 + - + -
100A PHE* 3.7 25.7 - - + +
119A LEU* 4.2 7.4 - - + -
127A ILE* 3.8 17.9 - - + +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU 3.0 11.5 + - - +
81A LEU* 3.5 13.9 - - + +
82A GLY 3.2 0.2 - - - -
83A ALA* 1.3 78.9 - - - +
85A ALA* 1.3 61.5 + - - +
86A VAL 3.6 0.2 + - - -
87A GLY* 3.8 7.1 + - - -
100A PHE* 3.9 19.1 - - + +
101A THR* 4.8 3.5 - - + +
102A TYR* 4.5 19.5 - - + +
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 5.3 7.0 - - - +
81A LEU 3.2 8.5 + - - +
82A GLY 3.1 8.9 + - - +
84A GLU* 1.3 82.4 - - - +
86A VAL* 1.3 63.4 + - + +
130A HIS* 4.9 8.2 + - + +
131A GLU* 4.1 15.3 - - - +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLY 3.0 17.7 + - - +
83A ALA* 4.4 2.5 - - - +
85A ALA* 1.3 79.1 - - - +
87A GLY* 1.3 61.9 + - - +
88A LEU* 4.2 16.6 - - + +
126A PHE* 3.6 29.4 - - + -
127A ILE* 4.0 20.9 - - + -
130A HIS* 3.6 42.0 - - + +
277A MET* 4.8 13.6 - - + +
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA 3.2 10.1 + - - -
84A GLU 3.8 5.8 + - - -
85A ALA 3.5 1.2 - - - -
86A VAL* 1.3 82.3 - - - +
88A LEU* 1.3 68.8 + - - +
89A VAL* 3.6 3.8 + - - +
99A ALA* 5.5 5.9 - - - +
100A PHE 5.1 5.6 - - - -
277A MET* 3.5 24.4 - - - +
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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