Contacts of the helix formed by residues 68 - 87 (chain D) in PDB entry 4CEV
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 LEU 68 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLN* 5.2 0.8 - - - -
65D LEU* 3.4 25.3 + - + +
66D ARG 3.1 2.0 - - - -
67D ASN* 1.3 76.7 - - - +
69D LYS* 1.3 61.6 + - + +
71D VAL* 3.9 0.2 - - - +
72D ALA* 2.8 34.2 + - + +
138D ILE* 3.7 12.3 - - + -
151D HIS* 3.5 39.5 - - + +
153D ALA* 4.0 13.0 - - + -
154D LEU* 3.6 39.7 - - + -
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Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D GLU* 3.2 44.2 + - + +
61D GLY 6.3 1.1 - - - +
67D ASN 3.2 0.8 - - - -
68D LEU* 1.3 81.0 - - + +
70D ALA* 1.3 57.7 + - - +
72D ALA* 3.3 4.2 + - - +
73D GLU* 2.9 32.8 + - - +
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 3.3 30.1 - - + +
51D ILE* 5.0 1.2 - - - +
52D GLY* 3.7 17.4 + - - +
53D LYS 4.5 1.6 - - - +
54D ALA* 4.0 17.9 - - - +
67D ASN 3.3 4.9 + - - +
69D LYS* 1.3 78.9 - - - +
71D VAL* 1.3 57.7 + - - +
73D GLU* 4.2 3.9 - - - +
74D ALA* 3.0 31.7 + - - +
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Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D MET* 3.8 9.8 - - + +
13D LEU* 3.6 39.7 - - + +
14D GLY* 4.2 2.9 - - - +
66D ARG 4.4 2.9 - - - +
67D ASN 2.9 23.8 + - - +
68D LEU 3.9 2.2 - - - +
70D ALA* 1.3 75.2 - - - +
72D ALA* 1.3 63.7 + - - +
75D ASN* 2.9 45.7 + - - +
100D SER* 3.8 13.9 - - - +
138D ILE* 3.8 26.7 - - + -
154D LEU* 4.5 4.5 - - + -
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LEU* 2.8 24.6 + - + +
69D LYS* 3.7 5.2 - - - +
71D VAL* 1.3 74.6 - - - +
73D GLU* 1.3 57.1 + - - +
75D ASN* 3.4 0.7 + - - -
76D GLU* 3.1 23.4 + - - +
153D ALA* 3.8 29.8 - - + +
154D LEU* 4.2 9.9 - - + -
157D ILE* 3.2 18.8 - - + +
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Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LYS 2.9 18.7 + - - +
70D ALA* 4.2 4.0 - - - +
72D ALA* 1.3 73.2 - - - +
74D ALA* 1.3 66.8 + - - +
76D GLU* 3.0 24.7 + - - +
77D LYS* 3.2 41.1 + - - +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 5.6 0.4 - - + -
11D MET* 3.6 17.0 - - + -
49D ILE* 3.7 4.4 - - - +
50D PRO 4.7 0.7 - - - -
51D ILE* 3.5 37.0 - - + -
52D GLY 5.4 0.4 - - - +
70D ALA 3.0 20.4 + - - +
71D VAL 3.9 0.2 - - - +
73D GLU* 1.3 75.1 - - - +
75D ASN* 1.3 58.2 + - - +
77D LYS* 3.2 16.9 + - - +
78D LEU* 3.0 26.8 + - - +
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Residues in contact with ASN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D MET* 4.1 6.2 - - - +
71D VAL* 2.9 39.6 + - - +
72D ALA* 3.7 5.3 - - - +
74D ALA* 1.3 74.2 - - - +
76D GLU* 1.3 60.4 + - - +
78D LEU* 3.8 5.9 - - - +
79D ALA* 2.9 29.5 + - - +
100D SER 3.1 21.3 + - - +
101D ILE* 3.3 15.0 - - - +
103D ILE* 3.9 9.6 - - + +
104D GLY* 2.7 34.6 + - - +
154D LEU* 5.3 0.6 - - - +
157D ILE* 3.6 13.1 - - + +
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Residues in contact with GLU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ALA 3.1 15.8 + - - +
73D GLU* 3.0 28.8 + - - +
75D ASN* 1.3 75.3 - - - +
77D LYS* 1.3 65.3 + - - +
79D ALA* 3.4 2.9 + - - +
80D ALA* 3.1 21.1 + - - +
156D GLN 4.2 1.9 - - - +
157D ILE* 3.2 22.4 - - + +
158D GLY* 3.2 27.5 + - - -
159D GLY 4.9 0.5 + - - -
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Residues in contact with LYS 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ILE* 3.8 15.0 - - + +
50D PRO* 3.4 39.8 + - + +
52D GLY 5.3 4.6 - - - +
73D GLU* 3.2 46.0 + - - +
74D ALA* 3.2 7.8 + - - +
76D GLU* 1.3 77.6 - - - +
78D LEU* 1.3 57.1 + - - +
80D ALA* 3.2 9.0 + - - +
81D ALA* 3.0 28.2 + - - +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE* 4.1 9.4 - - + -
9D VAL* 3.7 27.8 - - + -
49D ILE* 3.9 19.6 - - + +
74D ALA 3.0 16.1 + - - +
75D ASN* 3.7 7.6 - - - +
76D GLU 3.3 0.2 - - - -
77D LYS* 1.3 74.1 - - - +
79D ALA* 1.3 66.3 + - - +
81D ALA* 3.2 0.7 + - - +
82D VAL* 2.9 45.4 + - + +
94D VAL* 4.2 5.8 - - + -
101D ILE* 3.1 41.7 - - + +
104D GLY* 3.8 2.9 - - - -
105D THR* 3.4 20.2 - - - +
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ASN 2.9 18.8 + - - +
76D GLU* 3.7 7.2 - - - +
77D LYS 3.3 0.2 - - - -
78D LEU* 1.3 76.1 - - - +
80D ALA* 1.3 58.1 + - - +
83D ASP* 2.9 30.7 + - - +
104D GLY 3.3 21.3 - - - +
107D ALA* 3.7 19.5 - - + -
108D GLY* 3.4 8.7 - - - +
157D ILE* 4.0 7.2 - - + -
158D GLY* 4.9 5.4 - - - -
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Residues in contact with ALA 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLU 3.1 12.6 + - - +
77D LYS* 3.2 11.4 + - - +
79D ALA* 1.3 76.7 - - - +
81D ALA* 1.3 63.0 + - - +
83D ASP* 3.2 8.9 + - - +
84D GLN* 3.0 25.8 + - - +
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE* 3.8 16.1 - - + +
46D LEU* 5.2 1.4 - - + +
49D ILE* 3.8 21.8 - - + -
77D LYS 3.0 12.6 + - - +
78D LEU 3.2 7.6 + - - +
80D ALA* 1.3 76.4 - - - +
82D VAL* 1.3 61.5 + - - +
84D GLN* 3.5 11.2 + - - +
85D VAL* 3.2 26.7 + - - +
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE* 4.1 10.3 - - + -
78D LEU* 2.9 41.4 + - + +
79D ALA* 3.9 3.8 - - - +
81D ALA* 1.3 72.5 - - - +
83D ASP* 1.3 66.4 + - - +
85D VAL* 3.2 5.6 + - - +
86D VAL* 3.1 22.7 + - - +
92D PRO* 4.0 12.3 - - + -
94D VAL* 4.0 17.7 - - + -
105D THR* 3.7 15.5 - - + +
108D GLY* 3.9 5.6 - - - -
109D VAL* 3.5 32.1 - - + -
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Residues in contact with ASP 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ALA 2.9 19.8 + - - +
80D ALA* 3.4 9.2 - - - +
82D VAL* 1.3 76.2 - - - +
84D GLN* 1.3 58.0 + - - +
86D VAL 3.4 0.5 + - - -
87D GLN* 3.0 46.3 + - - +
108D GLY* 3.5 15.9 - - - +
111D LYS* 3.0 27.6 + - - +
112D HIS* 2.6 31.5 + - - -
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Residues in contact with GLN 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ALA 3.0 16.6 + - - +
81D ALA* 3.7 10.3 + - - +
83D ASP* 1.3 75.1 - - - +
85D VAL* 1.3 59.9 + - + +
87D GLN* 3.1 19.3 + - + +
88D ARG* 2.9 52.5 + - + +
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D SER* 3.6 24.2 - - - +
7D ILE* 3.9 8.7 - - + -
46D LEU* 3.5 31.0 - - + -
81D ALA 3.2 15.4 + - - +
82D VAL* 3.2 10.2 + - - +
84D GLN* 1.3 78.8 - - + +
86D VAL* 1.3 63.0 + - - +
88D ARG* 3.1 19.0 + - - +
90D ARG* 3.1 36.3 + - + +
92D PRO* 3.8 22.2 - - + -
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D VAL 3.1 14.9 + - - +
83D ASP 3.7 6.3 - - - +
85D VAL* 1.3 74.7 - - - +
87D GLN* 1.3 59.5 + - - +
89D GLY* 2.8 22.3 + - - -
90D ARG 3.8 8.3 - - - +
92D PRO* 4.0 26.0 - - + -
108D GLY 4.3 4.7 - - - +
109D VAL* 4.2 17.0 - - + -
112D HIS* 3.5 36.8 - - + +
113D TYR* 5.0 10.8 - - + +
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Residues in contact with GLN 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ASP* 3.0 40.4 + - - +
84D GLN* 3.1 20.8 + - - +
86D VAL* 1.3 78.1 - - - +
88D ARG* 1.3 58.5 + - + +
89D GLY* 3.0 4.4 + - - -
111D LYS* 5.1 3.0 - - - +
112D HIS* 3.7 16.5 - - + -
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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) + - + + + + + -
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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