Contacts of the helix formed by residues 64 - 77 (chain B) in PDB entry 4EVI
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 ALA 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 3.7 24.4 - - + +
51B ASN* 5.4 0.4 - - - -
54B ALA* 4.3 13.5 - - + -
60B PRO 3.4 3.6 + - - -
61B GLN* 3.1 29.7 + - - +
63B LYS* 1.3 77.5 - - - +
65B PRO* 1.4 60.5 - - + +
67B LEU* 3.1 10.5 + - - +
68B SER* 2.7 30.5 + - - -
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Residues in contact with PRO 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 4.9 2.0 - - + -
61B GLN 3.9 4.0 - - - +
62B THR 3.5 14.1 - - - +
63B LYS* 3.2 5.4 - - - -
64B ALA* 1.4 93.7 - - + +
66B PHE* 1.3 66.5 + - + +
68B SER* 3.4 8.4 - - - -
69B ARG* 3.2 31.8 + - - +
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Residues in contact with PHE 66 (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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137A TRP* 3.5 31.6 - + + -
138A LEU* 3.8 15.3 - - + -
149A PRO 4.6 7.4 - - - -
327A MET* 3.6 35.6 - - + +
331A GLU 6.1 2.7 - - - -
62B THR 4.5 5.6 - - - -
63B LYS* 2.9 33.4 + - + +
65B PRO* 1.3 79.0 - - + +
67B LEU* 1.3 66.8 + - - +
69B ARG* 3.1 29.1 + - - +
70B LEU* 3.0 21.1 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.4 5.2 - - + +
35B LEU* 5.2 0.2 - - + -
37B ILE* 4.7 1.3 - - + -
50B LEU* 4.0 11.9 - - + -
53B LEU* 4.0 15.0 - - + -
54B ALA* 3.7 39.7 - - + +
57B LEU* 3.9 21.3 - - + -
59B ILE* 4.0 18.2 - - + -
63B LYS 3.1 10.8 + - - +
64B ALA* 3.1 9.8 + - - +
66B PHE* 1.3 76.8 - - - +
68B SER* 1.3 61.6 + - - +
70B LEU* 3.2 20.5 + - + +
71B MET* 2.9 38.4 + - + +
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.9 15.7 - - - +
64B ALA 2.7 17.1 + - - -
65B PRO* 3.4 13.2 - - - -
66B PHE 3.2 0.2 - - - -
67B LEU* 1.3 74.0 - - - +
69B ARG* 1.3 58.5 + - - +
71B MET* 3.3 3.5 + - - +
72B ARG* 2.9 28.4 + - - +
82B GLN* 4.9 0.5 - - - +
96B PRO* 4.1 9.4 - - - +
98B TYR* 3.5 21.8 + - - -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 6.0 0.3 - - - +
323A ASP* 3.0 52.5 + - - +
324A MET* 3.2 17.0 - - + +
327A MET* 3.3 17.5 - - - +
331A GLU 5.9 0.6 - - - -
332A GLY* 2.9 27.9 + - - -
333A SER* 3.4 18.4 + - - +
65B PRO* 3.2 18.4 + - - +
66B PHE* 3.1 35.9 + - - +
68B SER* 1.3 78.1 - - - +
70B LEU* 1.3 62.3 + - - +
72B ARG* 3.3 22.1 + - - +
73B MET* 3.1 17.5 + - - +
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Residues in contact with LEU 70 (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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131A TRP* 5.0 3.8 - - + -
134A MET* 5.9 0.2 - - + -
138A LEU* 4.3 13.7 - - + -
324A MET* 3.6 23.3 - - + +
327A MET* 4.7 9.2 - - + -
28B THR* 4.3 29.4 - - + +
31B CYS* 4.6 11.7 - - + -
32B ALA 5.1 0.2 - - - +
35B LEU* 4.2 16.8 - - + -
37B ILE* 4.1 24.7 - - + -
66B PHE 3.0 12.9 + - - +
67B LEU* 3.5 14.6 - - + +
69B ARG* 1.3 77.2 - - - +
71B MET* 1.3 56.4 + - - +
73B MET* 3.2 5.0 + - - +
74B LEU* 3.0 39.6 + - + +
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Residues in contact with MET 71 (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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37B ILE* 3.8 31.6 - - - -
41B ILE* 3.9 16.4 - - + -
53B LEU* 4.1 14.6 - - + -
67B LEU* 2.9 22.6 + - + +
68B SER 3.6 5.4 - - - +
70B LEU* 1.3 73.4 - - - +
72B ARG* 1.3 54.9 + - - +
74B LEU* 3.1 7.3 + - - +
75B VAL* 2.7 40.6 + - - +
80B PHE* 3.6 30.1 - - + -
82B GLN* 4.1 0.4 - - - -
98B TYR* 3.3 51.4 - - + -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 3.3 29.5 - - - +
316A MET* 6.3 0.2 - - - -
320A LEU* 3.7 25.8 - - + +
323A ASP* 3.2 32.5 + - - -
333A SER* 4.1 5.7 + - - -
334A LEU 4.3 2.6 + - - -
336A THR* 4.2 13.3 - - - +
339A GLN* 5.2 4.4 + - - +
68B SER* 2.9 14.1 + - - +
69B ARG* 3.5 22.9 + - - +
70B LEU 3.3 0.4 - - - -
71B MET* 1.3 75.4 - - - +
73B MET* 1.3 61.6 + - - +
75B VAL* 3.5 3.5 + - - +
76B HIS* 3.1 22.2 + - - +
82B GLN* 3.6 24.4 + - - +
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Residues in contact with MET 73 (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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317A GLY 5.0 0.4 - - - +
320A LEU* 3.8 41.2 - - + +
321A ILE* 3.6 17.3 - - + -
324A MET* 3.8 20.2 - - + -
24B ILE* 4.2 9.0 - - + -
25B ASN* 3.0 28.7 - - - +
28B THR* 4.0 24.9 - - + +
69B ARG 3.1 12.3 + - - +
70B LEU 3.3 8.7 - - - +
71B MET 3.2 0.2 - - - -
72B ARG* 1.3 76.7 - - - +
74B LEU* 1.3 57.3 + - + +
76B HIS* 3.1 8.4 + - - +
77B LEU* 2.9 35.3 + - + +
402B GOL 3.9 6.1 - - - +
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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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28B THR* 4.1 17.0 - - - +
29B LEU* 4.6 3.6 - - + -
32B ALA* 3.9 31.2 - - + -
37B ILE* 4.1 9.4 - - + -
70B LEU* 3.0 42.1 + - + +
71B MET* 3.1 7.6 + - - +
73B MET* 1.3 73.0 - - + +
75B VAL* 1.3 65.7 + - - +
77B LEU* 3.3 22.8 + - + +
78B GLY 3.1 4.9 + - - -
79B TYR* 3.1 34.7 + - + +
80B PHE* 3.7 27.6 - - + -
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Residues in contact with VAL 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 MET 2.7 26.7 + - - +
72B ARG* 3.7 4.5 - - - +
74B LEU* 1.3 70.2 - - - +
76B HIS* 1.3 66.5 + - - +
78B GLY* 2.9 16.1 + - - -
80B PHE* 3.4 38.2 - - + +
81B THR* 4.0 17.9 - - + +
82B GLN* 3.5 29.4 - - + +
98B TYR* 4.7 2.7 - - + -
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Residues in contact with HIS 76 (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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313A SER* 3.4 34.9 + - - -
316A MET* 3.9 16.3 - - + +
317A GLY* 3.2 31.0 - - - -
320A LEU* 3.5 25.1 - - + +
72B ARG 3.1 4.6 + - - +
73B MET* 3.4 9.6 - - - +
75B VAL* 1.3 82.9 - - - +
77B LEU* 1.3 62.8 + - + +
78B GLY* 3.3 1.6 + - - -
402B GOL 3.6 22.6 + - - -
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Residues in contact with LEU 77 (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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15A GLN* 5.5 0.5 - - - +
19A HIS* 3.4 46.6 + - + +
25B ASN* 3.8 11.0 - - - +
28B THR* 4.2 18.8 - - - +
29B LEU* 5.3 2.2 - - + +
73B MET* 2.9 26.5 + - + +
74B LEU* 3.3 19.7 + - + +
75B VAL 3.2 0.6 - - - -
76B HIS* 1.3 77.9 - - + +
78B GLY* 1.3 58.9 + - - +
79B TYR* 3.6 17.9 - - + -
103B LEU* 3.8 7.3 - - - +
402B GOL 3.5 39.9 - - - +
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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