Contacts of the helix formed by residues 59 - 78 (chain H) in PDB entry 1VQ9
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 HIS 59 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H PRO* 5.2 5.2 - - + +
25H GLY 3.4 13.1 + - - -
26H SER* 3.4 21.1 - - - +
27H LYS* 2.8 54.3 - - + +
28H ILE* 3.8 5.3 - - + +
57H LEU 3.7 1.0 + - - -
58H ARG* 1.3 73.8 - - + +
60H GLY* 1.3 61.2 + - - +
62H LEU* 3.7 11.4 - - - -
63H GLU* 3.0 30.1 + - - +
91H PRO* 4.0 9.6 - - + -
121H VAL 5.3 1.8 - - - -
122H GLY* 4.4 9.2 - - - -
123H THR* 3.0 45.5 + - - +
124H ALA* 4.3 0.4 - - - +
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Residues in contact with GLY 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25180 C 5.1 0.7 + - - -
25190 C 3.4 26.9 - - - +
27H LYS* 4.1 26.0 - - - -
58H ARG* 3.1 5.3 + - - +
59H HIS* 1.3 84.7 + - - +
61H SER* 1.3 58.3 + - - +
63H GLU* 4.0 2.6 - - - +
64H ALA* 3.3 16.5 + - - +
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Residues in contact with SER 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25190 C 2.7 18.6 + - - -
25200 G 2.6 35.7 + - - -
57H LEU* 4.9 6.3 - - - -
58H ARG* 2.7 19.0 + - - +
60H GLY* 1.3 76.1 - - - +
62H LEU* 1.3 66.8 + - - +
63H GLU 3.2 1.1 - - - -
64H ALA* 3.8 1.3 - - - +
65H SER* 3.1 25.3 + - - -
156H LYS 3.9 8.9 - - - +
157H ILE* 4.2 8.4 - - - +
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Residues in contact with LEU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ILE* 3.6 26.5 - - + -
57H LEU* 2.9 39.3 - - + +
58H ARG 2.9 35.3 + - - +
59H HIS* 3.7 4.9 - - - +
61H SER* 1.3 76.4 - - - +
63H GLU* 1.3 58.7 + - - +
65H SER* 3.0 4.7 + - - +
66H ARG* 2.8 35.3 + - - +
87H LEU* 4.0 16.4 - - + -
89H LYS* 5.4 2.7 - - + +
91H PRO* 5.3 1.1 - - + -
125H ALA* 4.5 12.8 - - + +
133H LEU* 4.0 32.5 - - + -
134H PHE* 4.3 0.7 - - - -
157H ILE* 5.3 1.1 - - + -
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Residues in contact with GLU 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H LYS* 3.0 29.8 - - + +
28H ILE* 3.2 4.4 - - - +
29H ALA* 3.0 14.5 + - - +
59H HIS 3.0 16.7 + - - +
60H GLY* 4.1 4.5 - - - +
62H LEU* 1.3 78.8 - - - +
64H ALA* 1.3 57.3 + - - +
66H ARG* 2.9 46.8 + - - -
67H LEU* 2.9 51.5 + - + +
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Residues in contact with ALA 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25180 C 4.3 11.4 - - - +
25190 C 3.3 41.3 - - - +
60H GLY 3.3 14.7 + - - +
61H SER 3.8 0.9 - - - +
62H LEU 3.3 0.2 - - - -
63H GLU* 1.3 80.0 - - - +
65H SER* 1.3 57.9 + - - +
67H LEU* 3.6 5.4 - - - +
68H SER* 2.8 32.2 + - - -
156H LYS* 3.8 12.4 + - + +
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Residues in contact with SER 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H SER 3.1 11.2 + - - -
62H LEU* 3.0 12.0 + - - -
64H ALA* 1.3 76.4 - - - +
66H ARG* 1.3 75.1 + - - +
68H SER* 3.2 10.1 + - - -
69H ALA* 2.9 26.2 + - - +
134H PHE* 3.2 17.5 - - - -
153H ALA* 3.4 31.3 - - - +
156H LYS* 4.2 6.5 - - - +
157H ILE* 4.0 12.2 - - - +
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Residues in contact with ARG 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ILE* 3.9 1.5 - - - +
29H ALA* 2.9 14.3 - - - +
30H GLN* 2.7 62.9 + - - +
33H MET* 3.3 33.1 - - + -
62H LEU 2.8 18.4 + - - +
63H GLU* 2.9 41.8 + - - +
65H SER* 1.3 78.8 + - - +
67H LEU* 1.3 78.6 + - - +
69H ALA* 3.6 2.8 - - - +
70H ASN* 2.8 33.4 + - - +
85H MET* 4.0 0.9 - - + +
87H LEU* 4.3 8.1 - - + -
134H PHE* 3.5 23.1 - - + -
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Residues in contact with LEU 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H GLU* 2.9 33.7 + - + +
64H ALA* 3.6 5.8 - - - +
66H ARG* 1.3 96.9 - - - +
68H SER* 1.3 57.9 + - - +
69H ALA 2.8 5.0 + - - -
70H ASN* 4.9 2.2 - - + -
71H ARG* 2.8 69.6 + - + +
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Residues in contact with SER 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25020 C 6.0 0.4 - - - -
64H ALA 2.8 19.6 + - - -
65H SER* 3.2 12.0 + - - -
67H LEU* 1.3 72.4 - - - +
69H ALA* 1.3 57.6 + - - +
71H ARG* 4.3 19.1 - - - +
72H HIS* 4.1 7.3 + - - +
152H ARG* 3.5 45.9 + - - +
156H LYS* 3.6 23.4 - - - +
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Residues in contact with ALA 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H SER 2.9 16.3 + - - +
66H ARG* 3.6 4.0 - - - +
67H LEU 2.8 1.6 + - - -
68H SER* 1.3 78.0 - - - +
70H ASN* 1.3 67.3 + - - +
71H ARG 3.1 1.1 - - - -
72H HIS* 2.9 15.2 + - - +
73H LEU* 3.1 9.9 + - - +
85H MET* 4.1 15.7 - - + -
134H PHE* 5.6 1.8 - - + -
149H ALA* 3.2 37.3 - - + +
150H PHE* 5.0 1.6 - - + -
153H ALA* 3.9 9.0 - - + -
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Residues in contact with ASN 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H GLN* 4.7 6.1 + - - +
33H MET* 3.8 31.3 - - - +
66H ARG* 2.8 22.6 + - - +
67H LEU* 4.2 3.6 - - + +
69H ALA* 1.3 72.8 - - - +
71H ARG* 1.3 58.1 + - - +
73H LEU* 3.2 4.0 + - - +
74H ILE* 2.8 42.7 + - - +
83H TYR* 2.8 40.0 + - - -
85H MET* 3.6 15.5 - - + +
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Residues in contact with ARG 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25040 A 3.2 63.1 + - - -
25170 A 4.9 10.5 + - - -
67H LEU* 2.8 60.5 + - + +
68H SER* 4.3 19.2 - - - +
70H ASN* 1.3 77.3 - - - +
72H HIS* 1.3 57.5 + - - +
74H ILE* 3.5 13.1 + - + +
75H LYS* 3.1 26.8 + - + +
156H LYS* 5.1 4.2 - - - +
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Residues in contact with HIS 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H SER 4.1 10.8 + - - +
69H ALA 2.9 11.4 + - - +
71H ARG* 1.3 76.3 - - - +
73H LEU* 1.3 58.3 + - - +
74H ILE 3.0 4.7 - - - -
75H LYS* 2.9 16.4 + - + +
76H GLU* 2.9 57.4 + - + +
145H HIS* 3.5 26.9 + - - -
148H GLU* 3.7 24.5 - - + +
149H ALA* 3.9 15.5 - - + -
152H ARG* 4.2 30.2 + - - +
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Residues in contact with LEU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H ALA 3.1 4.6 + - - +
70H ASN* 3.2 8.0 + - - +
72H HIS* 1.3 79.1 - - - +
74H ILE* 1.3 56.7 + - - +
76H GLU* 3.9 2.0 - - - +
77H LEU* 2.9 44.1 + - + +
83H TYR* 3.5 41.2 - - + -
85H MET* 4.2 28.7 - - + -
136H ALA* 5.0 3.1 - - + -
138H CYS* 6.6 0.2 - - + -
142H ASP 5.4 0.7 - - - +
145H HIS* 3.6 33.4 - - + +
146H VAL* 3.9 21.5 - - + +
149H ALA* 3.9 12.1 - - + -
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Residues in contact with ILE 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H ASN* 2.8 36.7 + - + +
71H ARG* 3.5 11.2 - - + +
73H LEU* 1.3 75.1 - - - +
75H LYS* 1.3 62.2 + - - +
76H GLU 3.1 1.6 - - - -
78H GLY* 2.8 38.7 + - - +
79H GLU* 4.0 26.4 + - + +
83H TYR* 3.5 15.5 - - - +
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Residues in contact with LYS 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25040 A 4.7 13.8 + - - -
25050 G 4.8 10.3 + - - +
71H ARG* 3.1 17.0 + - + +
72H HIS* 2.9 16.0 + - + +
74H ILE* 1.3 78.6 - - + +
76H GLU* 1.3 73.3 + - + +
78H GLY 4.6 0.4 - - - -
152H ARG* 6.0 1.9 - - - +
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Residues in contact with GLU 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H HIS* 2.9 39.4 + - + +
73H LEU 4.5 0.7 - - - +
75H LYS* 1.3 95.7 - - + +
77H LEU* 1.3 76.8 + - + +
78H GLY 3.6 0.7 - - - -
145H HIS* 3.2 42.2 + - + +
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Residues in contact with LEU 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H LEU* 2.9 29.0 + - + +
76H GLU* 1.3 89.3 - - + +
78H GLY* 1.3 60.2 + - - +
81H GLY* 2.9 24.3 + - - -
82H ASP 4.7 4.0 - - - +
83H TYR* 3.4 38.6 - - + -
138H CYS* 5.4 0.4 - - + -
142H ASP* 3.0 50.5 - - + +
145H HIS* 3.7 17.5 - - + -
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Residues in contact with GLY 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H ILE* 2.8 26.5 + - - +
75H LYS 4.6 0.4 - - - -
76H GLU 3.6 1.6 - - - -
77H LEU* 1.3 78.9 - - - +
79H GLU* 1.3 54.9 + - - -
80H GLU 2.6 18.7 + - - -
81H GLY* 2.8 9.6 + - - -
83H TYR* 4.3 5.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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