Contacts of the helix formed by residues 68 - 87 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F GLN* 5.2 0.8 - - - -
62F ASP* 6.1 1.3 - - + -
65F LEU* 3.3 26.6 + - + +
66F ARG 3.1 2.4 + - - -
67F ASN* 1.3 76.4 - - - +
69F LYS* 1.3 65.3 + - + +
71F VAL* 3.9 0.2 - - - -
72F ALA* 2.8 33.8 + - - +
138F ILE* 3.7 11.2 - - + -
151F HIS* 3.7 37.2 - - + +
153F ALA* 4.0 13.5 - - + -
154F LEU* 3.6 39.5 - - + -
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Residues in contact with LYS 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F GLU* 4.6 22.4 - - + +
67F ASN 3.3 1.0 - - - -
68F LEU* 1.3 83.6 - - + +
70F ALA* 1.3 58.4 + - - +
72F ALA* 3.2 4.9 + - - +
73F GLU* 2.9 32.6 + - - +
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Residues in contact with ALA 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F MET* 4.7 0.2 - - - +
13F LEU* 3.3 30.3 - - + +
51F ILE* 5.1 0.3 - - - +
52F GLY* 3.5 17.5 + - - +
53F LYS 4.4 0.9 - - - +
54F ALA* 3.7 22.2 - - + +
67F ASN 3.3 2.9 + - - +
69F LYS* 1.3 77.4 - - - +
71F VAL* 1.3 57.9 + - - +
73F GLU* 4.0 4.9 - - - +
74F ALA* 3.1 30.5 + - - +
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Residues in contact with VAL 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F MET* 3.9 9.9 - - + -
13F LEU* 3.6 40.8 - - + +
14F GLY* 4.1 3.6 - - - +
67F ASN 2.9 22.4 + - - +
68F LEU 3.9 2.7 - - - +
70F ALA* 1.3 76.1 - - - +
72F ALA* 1.3 63.3 + - - +
74F ALA* 3.9 0.9 - - - +
75F ASN* 2.9 46.4 + - - +
100F SER* 3.7 13.7 - - - +
138F ILE* 3.8 29.6 - - + -
154F LEU* 4.5 4.7 - - + -
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Residues in contact with ALA 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F LEU 2.8 19.7 + - - +
69F LYS* 3.8 4.0 - - - +
71F VAL* 1.3 79.5 - - - +
73F GLU* 1.3 61.4 + - - +
75F ASN* 3.5 0.7 + - - -
76F GLU* 3.1 20.0 + - - +
153F ALA* 3.7 31.0 - - + +
154F LEU* 4.1 11.0 - - + -
157F ILE* 3.3 17.9 - - + +
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Residues in contact with GLU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLY 6.3 0.4 - - - +
69F LYS 2.9 17.3 + - - +
70F ALA* 4.0 4.9 - - - +
72F ALA* 1.3 74.2 - - - +
74F ALA* 1.3 66.8 + - - +
76F GLU* 3.1 22.0 + - - +
77F LYS* 2.9 50.5 + - - +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 5.6 1.8 - - + -
11F MET* 3.6 17.5 - - + -
49F ILE* 3.8 4.7 - - - +
51F ILE* 3.5 36.6 - - + -
52F GLY 5.4 0.2 - - - +
70F ALA 3.1 19.1 + - - +
73F GLU* 1.3 76.5 - - - +
75F ASN* 1.3 57.8 + - - +
77F LYS* 3.1 15.4 + - - +
78F LEU* 2.9 27.5 + - - +
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Residues in contact with ASN 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F MET* 4.2 5.0 - - - +
71F VAL* 2.9 37.4 + - - +
72F ALA* 3.8 5.3 - - - +
73F GLU 3.2 0.2 - - - -
74F ALA* 1.3 75.9 - - - +
76F GLU* 1.3 59.7 + - - +
78F LEU* 4.1 5.7 - - - +
79F ALA* 2.9 29.8 + - - +
100F SER 3.1 26.7 + - - +
101F ILE* 3.3 12.2 - - - +
103F ILE* 4.0 10.0 - - + +
104F GLY* 2.8 31.7 + - - +
154F LEU* 5.1 0.6 - - - +
157F ILE* 3.7 14.2 - - + +
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Residues in contact with GLU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F ALA 3.1 16.9 + - - +
73F GLU* 3.1 23.2 + - - +
75F ASN* 1.3 78.6 - - - +
77F LYS* 1.3 62.6 + - + +
79F ALA* 3.4 4.7 + - - +
80F ALA* 3.1 21.7 + - - +
156F GLN 4.4 1.6 - - - +
157F ILE* 3.3 17.4 - - + +
158F GLY* 3.2 31.4 + - - -
159F GLY 4.9 0.5 + - - -
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Residues in contact with LYS 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ILE* 3.8 15.7 - - + +
50F PRO* 3.4 40.3 + - + +
52F GLY 5.2 5.5 - - - +
73F GLU* 2.9 50.6 + - - +
74F ALA* 3.1 8.2 + - - +
76F GLU* 1.3 75.2 - - + +
78F LEU* 1.3 65.0 - - - +
80F ALA* 3.3 7.2 + - - +
81F ALA* 3.0 23.4 + - - +
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Residues in contact with LEU 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ILE* 4.0 15.7 - - + -
9F VAL* 3.7 28.3 - - + -
49F ILE* 4.1 11.8 - - + +
74F ALA 2.9 15.7 + - - +
75F ASN* 3.7 9.0 - - - +
77F LYS* 1.3 77.6 - - - +
79F ALA* 1.3 62.7 + - - +
81F ALA* 3.2 1.6 + - - +
82F VAL* 2.9 44.9 + - + +
94F VAL* 4.1 4.9 - - + -
101F ILE* 3.0 42.6 - - + +
104F GLY* 3.8 8.3 - - - -
105F THR* 3.5 13.7 - - - +
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Residues in contact with ALA 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ASN 2.9 18.7 + - - +
76F GLU* 3.5 8.3 - - - +
78F LEU* 1.3 77.3 - - - +
80F ALA* 1.3 56.5 + - - +
82F VAL* 3.4 0.4 + - - -
83F ASP* 2.8 31.7 + - - +
104F GLY 3.2 20.3 + - - +
107F ALA* 3.8 19.7 - - + -
108F GLY* 3.4 7.7 - - - +
157F ILE* 4.1 7.0 - - + -
158F GLY* 4.9 6.1 - - - -
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Residues in contact with ALA 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F GLU 3.1 10.8 + - - +
77F LYS* 3.6 10.3 - - - +
79F ALA* 1.3 80.2 - - - +
81F ALA* 1.3 63.8 + - - +
83F ASP* 3.2 9.0 + - - +
84F GLN* 3.0 24.3 + - - +
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ILE* 3.9 18.2 - - + -
46F LEU* 5.9 0.4 - - + -
49F ILE* 3.9 18.6 - - + -
77F LYS 3.0 13.4 + - - +
78F LEU 3.6 7.4 - - - +
80F ALA* 1.3 75.4 - - - +
82F VAL* 1.3 62.6 + - - +
84F GLN* 2.9 30.4 + - - +
85F VAL* 3.1 12.3 + - - +
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Residues in contact with VAL 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ILE* 4.0 10.3 - - + -
78F LEU* 2.9 42.8 + - + +
79F ALA* 3.8 4.0 - - - +
81F ALA* 1.3 72.1 - - - +
83F ASP* 1.3 65.7 + - - +
85F VAL* 3.2 6.1 + - - +
86F VAL* 3.0 21.8 + - - +
92F PRO* 3.9 12.3 - - + -
94F VAL* 4.0 16.6 - - + -
105F THR* 3.7 15.5 - - + +
108F GLY* 4.0 6.1 - - - -
109F VAL* 3.4 32.8 - - + -
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Residues in contact with ASP 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F ALA 2.8 19.1 + - - +
80F ALA* 3.3 9.8 - - - +
82F VAL* 1.3 75.8 - - - +
84F GLN* 1.3 62.7 + - - +
86F VAL* 3.2 3.8 + - - +
87F GLN* 3.0 41.4 + - - +
108F GLY* 3.5 16.7 + - - +
111F LYS* 2.8 32.4 + - - +
112F HIS* 2.7 27.1 + - - -
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Residues in contact with GLN 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU* 3.9 14.0 - - - +
80F ALA 3.0 12.2 + - - +
81F ALA* 2.9 27.4 + - - +
83F ASP* 1.3 76.2 - - - +
85F VAL* 1.3 67.4 + - - +
87F GLN* 3.1 15.8 + - - +
88F ARG* 2.9 66.3 + - + +
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Residues in contact with VAL 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F SER* 3.6 27.1 - - - +
7F ILE* 3.9 9.6 - - + -
46F LEU* 3.4 31.4 - - + -
81F ALA 3.1 13.8 + - - +
82F VAL* 3.5 9.0 - - - +
84F GLN* 1.3 81.0 - - - +
86F VAL* 1.3 63.9 + - - +
88F ARG* 3.2 14.5 + - - +
89F GLY 3.4 0.2 + - - -
90F ARG* 3.1 38.3 + - + +
92F PRO* 3.9 20.4 - - + -
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Residues in contact with VAL 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F VAL 3.0 14.8 + - - +
83F ASP 3.6 6.7 - - - +
85F VAL* 1.3 74.5 - - - +
87F GLN* 1.3 58.1 + - - +
89F GLY* 2.8 21.7 + - - -
90F ARG 3.9 7.7 + - - +
92F PRO* 4.1 24.7 - - + -
108F GLY 4.2 5.6 - - - +
109F VAL* 4.2 16.8 - - + -
112F HIS* 3.5 36.8 - - + +
113F TYR* 5.0 9.9 - - + +
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Residues in contact with GLN 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ASP* 3.0 40.8 + - - +
84F GLN* 3.1 15.8 + - - +
86F VAL* 1.3 76.9 - - - +
88F ARG* 1.3 58.4 + - + +
89F GLY* 3.1 5.0 + - - -
111F LYS* 5.5 1.0 - - - +
112F HIS* 3.7 16.1 - - + -
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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
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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