Contacts of the helix formed by residues 61 - 75 (chain A) in PDB entry 5J3V
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 ASP 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS* 2.7 28.5 + - - -
23A GLN* 4.9 2.3 - - - +
60A GLU* 1.3 76.5 - - - +
62A GLU* 1.3 63.6 + - - +
63A PRO* 3.3 20.6 - - + +
64A THR* 2.8 21.1 + - - -
65A ARG* 3.3 18.4 + - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLU 5.4 0.4 - - - +
61A ASP* 1.3 68.9 - - - +
63A PRO* 1.4 69.8 - - + +
64A THR 3.1 2.2 - - - -
65A ARG* 3.2 11.0 + - - +
66A SER* 2.8 31.7 + - - -
103A SER* 2.8 34.3 + - - +
105A LEU* 4.0 19.6 - - + +
106A ILE* 3.8 16.9 - - + +
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Residues in contact with PRO 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 3.2 21.1 + - - +
61A ASP* 3.3 22.7 - - + +
62A GLU* 1.4 93.9 - - + +
64A THR* 1.3 53.6 + - - +
66A SER* 3.9 2.7 - - - -
67A LEU* 3.1 21.7 + - - +
105A LEU* 4.1 14.1 - - + -
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU 5.3 0.9 - - - +
19A LEU* 3.9 32.8 - - + +
20A LYS* 2.9 19.5 + - + -
23A GLN* 3.8 16.6 + - - +
53A VAL* 4.8 2.2 - - + -
60A GLU* 3.8 19.7 - - - +
61A ASP* 2.8 30.4 + - - -
62A GLU 3.1 0.6 - - - -
63A PRO* 1.3 79.3 - - - +
65A ARG* 1.3 65.1 + - - +
66A SER 3.2 0.2 - - - -
67A LEU* 3.3 3.2 + - - +
68A SER* 3.1 23.6 + - - -
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL* 3.4 22.2 - - + +
54A LEU* 3.1 42.5 + - - +
55A THR* 4.4 1.0 + - - +
57A LEU 3.3 16.6 + - - +
58A LYS* 3.5 55.0 + - - +
60A GLU* 3.6 21.3 + - + +
61A ASP 3.3 12.1 + - - +
62A GLU* 3.2 14.5 + - - +
64A THR* 1.3 75.9 - - - +
66A SER* 1.3 60.5 + - - +
68A SER* 2.8 21.3 + - - -
69A GLY 3.4 1.2 + - - -
98A ASN* 5.5 0.2 - - - +
101A ASP* 4.6 1.4 + - - -
103A SER* 6.2 0.2 - - - -
106A ILE* 3.8 29.2 - - + +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.4 1.8 - - - -
62A GLU 2.8 17.0 + - - -
63A PRO* 4.0 4.9 - - - -
65A ARG* 1.3 75.6 - - - +
67A LEU* 1.3 64.6 + - - +
69A GLY 3.2 1.9 + - - -
70A LEU* 3.0 39.1 + - - +
105A LEU* 3.9 27.5 - - - +
106A ILE* 4.1 3.3 - - - +
109A THR* 2.9 30.8 + - - +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.8 14.1 - - + +
22A SER* 3.3 28.7 - - - +
23A GLN* 3.7 26.2 - - + +
63A PRO 3.1 19.9 + - - +
64A THR 3.3 5.1 + - - +
66A SER* 1.3 76.7 - - - +
68A SER* 1.3 51.9 + - - +
70A LEU* 3.0 14.4 + - + -
71A ILE* 2.7 56.7 + - + +
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.9 24.0 - - - +
50A LEU* 3.3 36.3 + - - +
53A VAL* 3.5 15.6 - - - +
54A LEU 3.8 1.0 + - - -
64A THR 3.1 12.5 + - - -
65A ARG 2.8 21.1 + - - -
67A LEU* 1.3 76.4 - - - +
69A GLY* 1.3 56.1 + - - +
71A ILE* 3.4 6.7 + - - +
72A LEU* 2.9 28.1 + - - +
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Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU 4.6 1.3 - - - -
54A LEU* 4.0 19.3 - - - -
65A ARG 3.4 1.8 + - - -
66A SER 3.2 8.3 + - - -
68A SER* 1.3 83.2 + - - +
70A LEU* 1.3 56.8 + - - +
72A LEU* 3.5 6.2 - - - +
73A LYS* 3.2 17.3 + - - +
109A THR* 3.9 16.5 - - - +
113A LEU* 3.4 18.5 - - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A SER* 3.0 35.0 + - - +
67A LEU* 3.6 13.5 - - + +
69A GLY* 1.3 77.4 - - - +
71A ILE* 1.3 65.6 + - - +
72A LEU 3.2 1.1 - - - -
73A LYS* 3.4 27.6 + - - +
74A ASN* 3.2 29.7 + - - +
109A THR* 4.0 16.6 - - + +
112A ILE* 4.1 16.4 - - + -
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Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 5.0 3.1 - - + -
22A SER* 6.5 0.7 - - - -
34A GLN* 6.2 3.8 - - + -
37A LEU* 4.3 35.7 - - + -
46A PHE* 5.3 1.1 - - + -
50A LEU* 4.0 19.5 - - + -
67A LEU* 2.7 39.6 + - + +
68A SER* 3.4 8.5 + - - +
70A LEU* 1.3 76.1 - - - +
72A LEU* 1.3 63.6 + - - +
74A ASN* 3.3 15.2 + - + +
75A ASN* 3.0 37.0 + - - +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASN* 3.3 39.3 - - + +
50A LEU* 3.7 12.8 - - + +
51A ILE* 3.8 32.5 - - + +
68A SER 2.9 18.1 + - - +
69A GLY* 3.5 6.5 - - - +
71A ILE* 1.3 78.0 - - - +
73A LYS* 1.3 62.5 + - - +
75A ASN* 3.0 13.6 + - - +
76A VAL* 3.1 20.1 + - + +
83A PHE* 4.5 3.8 - - + -
91A ILE* 3.7 25.1 - - + -
113A LEU* 3.9 26.5 - - + -
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLY 3.2 12.8 + - - +
70A LEU* 3.5 28.0 - - + +
71A ILE 3.2 0.4 - - - -
72A LEU* 1.3 79.3 - - - +
74A ASN* 1.3 85.7 + - - +
76A VAL* 2.9 20.0 + - - +
77A LYS* 3.0 30.4 + - + +
112A ILE* 3.6 39.9 - - + -
113A LEU* 3.7 14.3 - - + +
116A THR* 3.7 23.6 - - + +
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Residues in contact with ASN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.2 16.8 + - - +
71A ILE* 3.7 17.4 - - + +
73A LYS* 1.3 103.6 + - - +
75A ASN* 1.3 60.8 + - - +
76A VAL 3.1 0.7 - - - -
77A LYS* 3.9 16.2 + - - +
78A ALA* 3.4 25.8 + - - +
79A HIS* 5.1 0.7 + - - -
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU 4.3 4.9 + - - +
41A ASN* 3.3 35.6 + - - +
46A PHE* 3.8 19.2 - - - -
47A ASN* 3.3 22.1 + - - +
50A LEU* 3.9 4.9 - - - +
71A ILE* 3.0 19.4 + - - +
72A LEU 3.0 10.8 + - - +
74A ASN* 1.3 79.4 - - - +
76A VAL* 1.3 57.0 + - - +
78A ALA 2.8 19.9 - - - +
79A HIS* 3.9 2.7 + - - +
83A PHE* 3.1 21.1 - - - -
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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
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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