Contacts of the helix formed by residues 67 - 83 (chain H) in PDB entry 1VCB
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 67 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G PHE* 3.7 12.6 - - - -
94G SER* 3.2 15.5 + - - -
23H SER* 3.3 6.9 + - - -
25H ASP* 2.4 40.5 + - - -
27H HIS* 2.6 27.4 + - - -
29H PHE* 4.0 6.0 - - - -
66H PRO* 1.3 67.4 - - - +
68H HIS* 1.3 58.8 + - - +
69H VAL 3.0 4.7 - - - -
70H LEU 4.6 0.2 - - - +
71H SER* 3.0 34.7 + - - -
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Residues in contact with HIS 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G PHE* 3.9 8.0 - - + +
94G SER* 2.5 46.3 + - - +
95G SER 4.0 12.8 - - - -
96G PRO* 3.4 32.2 - - + +
97G PRO* 5.1 0.2 - - + -
66H PRO* 3.3 29.1 - - + +
67H SER* 1.3 77.6 - - - +
69H VAL* 1.3 62.9 + - + +
71H SER* 3.7 12.9 + - - -
72H LYS* 4.3 5.7 - - - +
99H ILE* 3.8 32.6 - - + +
102H GLU* 3.1 28.5 + - - -
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Residues in contact with VAL 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ILE* 3.3 25.4 - - + -
66H PRO* 3.1 17.8 + - + +
67H SER 3.0 0.8 - - - -
68H HIS* 1.3 90.8 - - + +
70H LEU* 1.3 59.2 + - - +
71H SER 3.1 1.3 - - - -
72H LYS* 2.8 26.3 + - - +
73H VAL* 3.1 10.4 + - + +
99H ILE* 5.0 6.3 - - + +
102H GLU* 3.5 31.6 - - + +
103H LEU* 4.0 16.2 - - + +
106H ALA* 3.5 22.9 - - + -
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Residues in contact with LEU 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LEU* 4.0 15.7 - - + +
22H ILE 3.8 6.7 - - - -
23H SER* 3.7 30.1 - - - +
29H PHE* 3.8 24.7 - - + -
62H PHE* 4.0 18.4 - - + -
65H ILE* 3.8 17.0 - - + +
66H PRO 2.9 18.9 + - - +
69H VAL* 1.3 73.6 - - - +
71H SER* 1.3 61.1 + - - +
73H VAL* 3.8 24.0 - - + -
74H CYS* 3.1 34.2 + - - -
110H LEU* 5.4 1.6 - - + -
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Residues in contact with SER 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G PHE* 3.8 5.9 - - - -
93G PHE* 3.6 32.6 - - - -
29H PHE* 3.9 15.0 - - - -
67H SER 3.0 19.4 + - - -
68H HIS* 3.7 9.9 + - - -
69H VAL 2.9 0.4 + - - -
70H LEU* 1.3 77.8 - - - +
72H LYS* 1.3 65.1 + - - +
74H CYS* 3.4 2.9 + - - +
75H MET* 3.1 39.7 + - - +
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Residues in contact with LYS 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G GLN 4.1 11.1 + - - -
68H HIS 4.3 11.2 - - - +
69H VAL 2.8 11.1 + - - +
71H SER* 1.3 81.0 + - - +
73H VAL* 1.3 58.9 + - - +
75H MET* 3.1 19.4 + - + +
76H TYR* 2.8 30.2 + - - +
93H PHE* 3.8 20.4 - - + -
94H PRO* 2.9 42.4 + - - +
95H ILE* 4.8 6.3 - - - +
96H ALA* 5.2 1.8 - - - +
99H ILE* 4.4 24.0 - - + -
103H LEU* 4.1 20.0 - - + -
158I LEU* 5.7 0.2 - - - -
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Residues in contact with VAL 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ILE* 5.6 0.7 - - + -
65H ILE* 5.3 0.7 - - + -
69H VAL* 3.1 18.1 + - + +
70H LEU* 3.6 23.6 - - + +
71H SER 3.4 0.2 - - - -
72H LYS* 1.3 76.1 - - - +
74H CYS* 1.3 65.4 + - - +
76H TYR* 3.0 18.5 + - - +
77H PHE* 3.0 43.9 + - + -
103H LEU* 3.9 19.5 - - + -
106H ALA* 4.5 3.1 - - + -
110H LEU* 3.6 27.6 - - + -
158I LEU* 4.3 10.3 - - + -
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Residues in contact with CYS 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G PHE* 3.5 28.9 - - + -
21H LEU* 3.8 17.0 - - - -
29H PHE* 3.8 20.2 - - - -
31H VAL* 3.6 26.7 - - + +
70H LEU* 3.1 21.8 + - - +
72H LYS 3.2 0.2 - - - -
73H VAL* 1.3 78.5 - - - +
75H MET* 1.3 63.1 + - - +
77H PHE* 3.0 22.2 + - - +
78H THR* 3.3 15.8 + - - +
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Residues in contact with MET 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G MET* 3.9 31.0 - - + -
15G PHE* 3.8 15.0 - - + -
69G PRO 3.5 10.0 - - - +
70G GLN 3.7 22.0 - - - +
71G ALA* 4.7 1.8 - - - -
72G PRO* 3.9 13.7 - - + -
93G PHE* 5.5 2.0 - - + -
71H SER* 3.1 28.7 + - - +
72H LYS* 3.1 27.3 + - + +
74H CYS* 1.3 76.7 - - - +
76H TYR* 1.3 61.2 + - - +
78H THR* 3.2 11.0 + - - -
79H TYR* 3.1 22.2 + - - +
93H PHE* 4.1 6.4 - - + -
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Residues in contact with TYR 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H THR* 4.4 8.1 - - + -
72H LYS 2.8 12.7 + - - +
73H VAL* 3.0 12.3 + - - +
75H MET* 1.3 75.9 - - - +
77H PHE* 1.3 74.3 + + - +
79H TYR* 3.3 21.7 - + - +
80H LYS* 2.8 56.1 + - + +
93H PHE* 3.6 23.5 - + + -
112H CYS* 3.7 15.9 + - + -
155I VAL* 4.0 2.8 + - - +
156I TYR 2.7 29.5 + - - -
157I THR* 3.3 9.7 - - - -
158I LEU* 3.5 38.4 - - + -
161I ARG* 5.7 1.3 - - + -
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Residues in contact with PHE 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LEU* 4.3 10.1 - - + -
31H VAL* 4.7 8.1 - - + -
35H HIS* 3.5 30.7 - - + +
36H ALA* 3.7 19.5 - - + -
38H THR* 3.9 19.3 - - + -
39H SER* 4.0 19.7 - - - -
42H ILE* 4.1 15.0 - - + -
73H VAL* 3.0 43.5 + - + -
74H CYS* 3.0 16.2 + - - +
76H TYR* 1.3 84.1 - + - +
78H THR* 1.3 62.2 + - + +
80H LYS* 4.0 3.3 - - - +
81H VAL* 3.1 29.8 + - - +
110H LEU* 4.9 0.7 - - + -
112H CYS* 4.1 20.4 - - - -
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Residues in contact with THR 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G PHE* 4.8 15.1 - - + +
15G PHE* 4.5 27.4 - - + -
16G THR* 6.4 0.9 - - - -
69G PRO* 3.1 32.8 + - - +
72G PRO* 5.9 1.0 - - - +
31H VAL* 5.5 1.8 - - + -
35H HIS* 3.6 28.4 + - + -
74H CYS 3.3 12.0 + - - +
75H MET* 3.2 4.7 + - - -
77H PHE* 1.3 76.7 - - + +
79H TYR* 1.3 56.0 + - - +
81H VAL* 3.4 1.9 + - - +
82H ARG* 2.8 33.1 + - - +
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Residues in contact with TYR 79 (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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69G PRO* 3.8 11.2 - - + -
70G GLN* 3.3 30.1 - - + +
75H MET 3.1 14.5 + - - +
76H TYR* 3.3 25.1 - + - +
78H THR* 1.3 78.0 + - - +
80H LYS* 1.3 67.5 + - - +
82H ARG 3.3 0.5 + - - -
83H TYR* 3.0 53.4 + + - +
90H ILE* 3.5 14.2 - - + +
91H PRO 2.7 28.8 + - - -
92H GLU* 4.4 0.2 - - - -
93H PHE* 3.8 35.1 + + + +
153I LEU* 5.0 1.6 - - - +
154I PRO 4.7 4.7 + - - -
155I VAL* 4.0 20.0 - - + -
156I TYR 5.2 1.7 + - - -
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Residues in contact with LYS 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H THR* 3.9 32.1 + - + +
76H TYR* 2.8 46.5 + - + +
77H PHE 4.0 2.7 - - - +
79H TYR* 1.3 73.5 - - - +
81H VAL* 1.3 69.2 + - - +
82H ARG 3.1 0.2 + - - -
84H THR* 3.1 55.8 + - + +
155I VAL* 4.2 12.6 - - + -
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Residues in contact with VAL 81 (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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34H GLU* 4.8 4.3 - - + +
35H HIS* 3.7 42.4 - - + +
38H THR* 3.7 19.3 - - - +
77H PHE 3.1 18.4 + - - +
78H THR 4.0 2.7 - - - +
80H LYS* 1.3 84.3 - - + +
82H ARG* 1.3 62.7 + - - +
84H THR* 4.6 8.1 + - - +
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Residues in contact with ARG 82 (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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1G MET* 5.8 9.1 - - - +
2G ASP* 5.6 4.6 + - - +
4G PHE* 4.0 26.1 - - + -
69G PRO* 3.9 23.0 - - + +
78H THR 2.8 18.9 + - - +
79H TYR 3.8 3.1 - - - +
81H VAL* 1.3 82.1 - - - +
83H TYR* 1.3 87.7 + - + +
84H THR 4.6 1.4 - - - +
86H SER* 4.1 9.0 + - - -
88H THR* 4.0 20.0 + - - +
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Residues in contact with TYR 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ARG* 5.1 3.1 + - - -
69G PRO* 4.2 8.8 - - + +
70G GLN* 3.8 13.0 + - - -
79H TYR* 3.0 46.4 + + + +
82H ARG* 1.3 118.4 + - + +
84H THR* 1.3 68.9 + - - +
85H ASN 3.3 1.4 + - - -
86H SER* 3.1 18.8 + - - -
88H THR* 4.4 7.4 - - - -
89H GLU 4.4 7.0 - - - -
90H ILE* 3.8 36.9 - - + +
91H PRO* 3.5 37.0 - - + +
155I VAL* 3.8 8.1 - - + -
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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) + - + + + + + -
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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