Contacts of the helix formed by residues 61 - 77 (chain B) in PDB entry 3HV4
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 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 6.4 1.6 - - - -
120A GLN* 4.2 7.2 - - - -
159A ASN 5.3 1.1 - - - -
160A GLU* 2.8 35.1 + - - -
162A CYS* 4.8 6.1 - - - -
59B PHE 3.9 3.3 - - - -
60B GLN* 1.3 78.0 - - - +
62B ILE* 1.3 61.7 + - - +
63B ILE 3.8 2.5 + - - -
64B HIS* 3.3 20.9 + - - +
65B ALA* 3.2 23.4 + - - +
334B ILE* 3.9 9.9 - - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B SER* 1.3 71.5 - - - +
63B ILE* 1.3 75.8 + - + +
64B HIS 3.1 1.3 - - - -
65B ALA* 2.9 6.0 + - - +
66B LYS* 2.9 32.7 + - + +
332B LEU 3.1 28.7 - - - +
333B LEU* 4.1 4.7 - - + -
334B ILE* 4.0 27.5 - - + +
337B TRP* 4.5 9.1 - - + +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 3.4 37.7 - - + -
61B SER* 3.6 1.0 + - - +
62B ILE* 1.3 89.4 - - + +
64B HIS* 1.3 58.2 + - + +
66B LYS* 3.5 12.0 + - + +
67B ARG* 3.1 63.3 + - + +
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Residues in contact with HIS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 3.1 23.2 + - + -
161A ASP* 3.0 34.4 + - - -
162A CYS* 6.1 1.1 - - - -
34B ALA 3.9 14.8 + - - -
35B TYR* 5.8 0.6 - - - -
56B SER* 3.0 30.5 + - - -
57B ARG* 3.0 20.3 + - + +
58B PRO* 3.1 13.0 - - + +
60B GLN* 5.4 0.2 - - - +
61B SER* 3.3 18.5 + - - +
62B ILE 3.1 0.6 - - - -
63B ILE* 1.3 75.7 - - - +
65B ALA* 1.3 60.6 + - - +
67B ARG* 3.6 19.2 + - - +
68B THR* 2.9 34.7 + - - -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO 3.3 8.9 + - - +
59B PHE* 4.5 8.6 - - + -
61B SER 3.2 15.7 + - - +
62B ILE* 2.9 12.3 + - - +
64B HIS* 1.3 74.5 - - - +
66B LYS* 1.3 64.2 + - - +
68B THR* 3.6 1.6 + - - -
69B TYR* 3.4 15.9 + - - +
334B ILE* 4.1 16.2 - - + +
337B TRP* 3.6 39.4 - - + +
341B THR* 4.8 0.7 + - - -
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 2.9 16.0 + - + +
63B ILE* 3.8 15.0 - - + +
64B HIS 3.3 0.2 - - - -
65B ALA* 1.3 72.4 - - - +
67B ARG* 1.3 67.5 + - + +
68B THR 3.2 0.5 + - - -
69B TYR* 3.3 4.7 + - - +
70B ARG* 2.9 33.4 + - - +
327B PHE* 5.9 1.0 - - - -
328B GLU* 2.8 54.5 + - - +
330B ARG 4.0 12.8 - - - -
337B TRP* 3.8 35.1 - - + +
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Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 3.0 23.6 + - - -
161A ASP* 3.5 17.8 + - - -
35B TYR* 3.1 50.5 + - - +
55B LEU* 5.5 0.2 - - - -
63B ILE* 3.1 41.0 + - + +
64B HIS* 3.6 16.1 + - - +
66B LYS* 1.3 81.3 - - + +
68B THR* 1.3 57.0 + - - +
70B ARG* 3.4 16.0 + - - +
71B GLU* 3.0 28.1 + - - +
361B L51 3.5 28.0 - - + +
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.5 33.4 - - + +
58B PRO* 3.3 18.5 + - + +
59B PHE* 3.8 19.1 - - + -
64B HIS 2.9 20.5 + - - -
65B ALA 4.0 4.7 - - - -
66B LYS 3.2 0.4 - - - -
67B ARG* 1.3 74.6 - - - +
69B TYR* 1.3 65.6 + - - +
71B GLU* 4.2 1.4 - - - +
72B LEU* 3.2 23.5 + - + +
102B VAL* 3.8 18.8 - - + -
341B THR* 3.8 11.7 - - + -
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Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA 3.4 5.3 + - - +
66B LYS 3.3 5.2 + - - +
68B THR* 1.3 79.2 - - - +
70B ARG* 1.3 62.5 + - - +
72B LEU* 4.1 0.2 - - - -
73B ARG* 2.8 63.9 + - + +
327B PHE* 3.5 33.9 - + - -
337B TRP* 3.5 39.0 - + + +
340B LEU* 3.7 29.5 - - + +
341B THR* 3.5 33.4 + - - +
344B GLU* 3.6 23.6 + - + -
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS* 2.9 23.3 + - - +
67B ARG* 3.6 25.3 - - - +
69B TYR* 1.3 77.4 - - - +
71B GLU* 1.3 52.5 + - - +
73B ARG* 3.6 1.0 - - - +
74B LEU* 2.7 44.0 + - + +
325B GLN* 5.0 7.7 - - - +
327B PHE* 4.0 29.3 - - + -
361B L51 3.5 31.3 - - + +
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS* 2.8 28.8 + - - -
55B LEU* 3.7 9.5 - - + +
67B ARG 3.0 13.0 + - - +
68B THR* 4.3 2.5 - - - +
70B ARG* 1.3 78.1 - - - +
72B LEU* 1.3 58.8 + - - +
74B LEU* 4.5 0.9 - - - -
75B LEU* 2.8 37.9 + - + +
104B LEU* 3.7 18.6 - - + +
361B L51 2.5 80.8 + - + +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR 3.2 16.7 + - - +
69B TYR 4.2 1.1 - - - +
71B GLU* 1.3 76.5 - - - +
73B ARG* 1.3 67.2 + - - +
75B LEU* 4.0 0.6 - - - -
76B LYS* 3.0 30.9 + - + +
86B LEU* 3.7 26.0 - - + -
89B VAL* 3.7 21.5 - - + -
102B VAL* 4.9 4.0 - - + -
104B LEU* 3.8 15.7 - - + +
341B THR* 3.8 13.2 - - + -
344B GLU* 3.7 22.0 - - + -
345B VAL* 3.7 32.3 - - + +
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 2.8 55.0 + - + +
70B ARG* 3.7 2.5 - - - +
72B LEU* 1.3 76.5 - - - +
74B LEU* 1.3 64.3 + - - +
76B LYS* 3.6 8.7 + - - +
77B HIS* 3.0 32.4 + - + +
323B TYR* 3.7 30.4 - - - +
324B ASP* 3.0 37.7 + - - +
325B GLN* 3.4 8.7 + - - +
327B PHE* 3.6 24.1 - - - -
344B GLU* 3.9 17.9 + - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 2.7 29.7 + - + +
71B GLU* 3.9 3.1 - - - +
73B ARG* 1.3 72.3 - - - +
75B LEU* 1.3 62.7 + - + +
77B HIS* 2.9 23.6 + - - +
78B MET* 3.3 39.1 + - + +
146B ILE* 2.9 42.0 - - + -
325B GLN* 3.7 17.9 - - + +
361B L51 4.0 47.3 - - + +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 2.8 34.4 + - + +
72B LEU* 4.3 1.6 - - - +
74B LEU* 1.3 75.3 - - + +
76B LYS* 1.3 62.1 + - - +
77B HIS 3.0 1.4 + - - -
78B MET* 3.2 24.3 + - + +
84B ILE* 4.1 16.4 - - + +
85B GLY 5.5 1.6 - - - +
86B LEU* 4.0 35.2 + - + +
104B LEU* 4.5 6.5 - - + -
106B THR* 5.4 3.4 - - + -
361B L51 3.6 78.5 - - + +
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.0 35.8 + - + +
73B ARG* 3.8 7.2 - - - +
74B LEU 3.1 0.4 + - - -
75B LEU* 1.3 76.2 - - - +
77B HIS* 1.3 70.8 + - + +
78B MET 3.7 0.8 + - - -
79B LYS* 3.2 25.3 + - - -
86B LEU* 3.8 15.7 - - + +
344B GLU* 2.4 68.0 + - + +
347B SER* 3.6 13.1 + - - -
348B PHE* 4.0 26.8 - - + +
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Residues in contact with HIS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 3.0 30.0 + - + +
74B LEU 2.9 2.5 + - - +
76B LYS* 1.3 92.4 + - + +
78B MET* 1.3 67.6 + - + +
79B LYS* 3.3 8.0 + - - +
140B TYR* 2.9 16.5 + - - -
320B ALA* 5.9 0.3 - - - +
321B ASP* 2.8 33.4 + - - +
323B TYR* 3.2 47.5 - + + -
325B GLN* 3.4 25.1 - - + +
344B GLU* 5.1 6.5 + - - -
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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
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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