Contacts of the helix formed by residues 62 - 76 (chain A) in PDB entry 1R00
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 HIS 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A THR* 1.3 70.9 - - - +
63A PRO* 1.3 69.8 - - + +
64A GLN* 3.8 23.7 + - + -
65A ALA* 3.2 32.3 + - + +
66A LEU* 2.8 29.9 + - - +
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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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52A LEU* 3.4 20.3 - - + +
53A ALA* 5.6 7.4 - - + -
56A ALA* 3.9 22.2 - - + -
57A ASP* 6.1 0.4 - - - +
61A THR 3.2 8.9 - - - +
62A HIS* 1.3 88.9 - - + +
64A GLN* 1.3 64.1 + - - +
66A LEU* 3.2 0.8 + - + -
67A SER* 3.0 19.6 + - - -
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Residues in contact with GLN 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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52A LEU* 5.3 0.4 - - - -
62A HIS* 3.3 20.9 + - + +
63A PRO* 1.3 79.2 - - - +
65A ALA* 1.3 61.7 + - - +
67A SER* 3.0 27.9 + - - +
68A ARG* 3.1 32.1 + - - +
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Residues in contact with ALA 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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62A HIS* 3.2 28.4 + - + +
64A GLN* 1.3 76.3 - - - +
66A LEU* 1.3 65.7 + - - +
68A ARG* 3.2 16.2 + - - +
69A LEU* 3.0 21.4 + - - +
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Residues in contact with LEU 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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39A LEU* 4.2 15.9 - - + -
41A LEU* 4.4 6.5 - - + -
52A LEU* 3.7 11.2 - - + -
55A LEU* 3.8 20.6 - - + -
56A ALA* 3.6 29.8 - - - +
59A THR* 4.3 1.8 - - - +
61A THR* 3.7 20.8 - - - +
62A HIS 2.8 17.4 + - - +
63A PRO* 3.2 6.5 + - + +
65A ALA* 1.3 71.7 - - - +
67A SER* 1.3 56.2 - - - +
69A LEU* 3.1 24.7 + - + +
70A VAL* 2.7 48.1 + - + +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.2 34.9 - - - +
63A PRO 3.0 7.7 + - - -
64A GLN* 3.0 17.1 + - - +
66A LEU* 1.3 74.3 - - - +
68A ARG* 1.3 61.7 + - - +
70A VAL* 3.3 5.5 + - - +
71A ARG* 2.7 46.5 + - - +
84A LYS* 5.9 1.5 + - - -
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Residues in contact with ARG 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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64A GLN* 3.1 39.6 + - + +
65A ALA* 3.5 13.0 - - - +
66A LEU 3.1 0.6 - - - -
67A SER* 1.3 84.9 + - - +
69A LEU* 1.3 59.7 + - - +
71A ARG* 3.6 37.4 + - - +
72A HIS* 3.4 19.6 + - - +
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Residues in contact with LEU 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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32A ALA* 3.6 40.8 - - + +
35A VAL* 3.9 28.3 - - + -
36A ALA 4.8 0.2 - - - +
39A LEU* 4.7 0.9 - - + -
41A LEU* 4.1 9.6 - - + -
65A ALA 3.0 12.3 + - - +
66A LEU* 3.1 27.8 + - + +
68A ARG* 1.3 74.5 - - - +
70A VAL* 1.3 59.2 + - - +
72A HIS* 3.3 6.3 + - + +
73A LEU* 2.9 46.9 + - + +
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Residues in contact with VAL 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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41A LEU* 4.8 4.7 - - + -
52A LEU* 5.0 3.4 - - + -
55A LEU* 4.5 7.9 - - + -
66A LEU* 2.7 40.5 + - + +
67A SER* 3.6 7.6 - - - +
69A LEU* 1.3 71.0 - - - +
71A ARG* 1.3 67.3 + - - +
73A LEU* 3.0 7.6 + - - +
74A THR* 2.9 29.5 + - - +
79A LEU* 4.0 14.6 - - + -
89A LEU* 3.7 43.1 - - + -
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Residues in contact with ARG 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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67A SER* 2.7 26.8 + - - +
68A ARG* 3.6 40.7 + - - +
70A VAL* 1.3 74.8 - - - +
72A HIS* 1.3 62.7 + - - +
74A THR* 3.1 7.8 + - - -
75A VAL* 3.1 26.0 + - + +
84A LYS* 3.5 33.3 - - - +
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Residues in contact with HIS 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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26A ASN* 5.2 0.4 + - - -
28A VAL* 4.3 15.9 - - + +
29A THR* 2.9 44.5 + - + -
32A ALA* 4.0 14.8 - - + +
68A ARG 3.4 10.0 + - - +
69A LEU* 3.3 10.4 + - - +
70A VAL 3.1 0.6 - - - -
71A ARG* 1.3 80.7 - - - +
73A LEU* 1.3 63.5 + - - +
74A THR 3.1 0.3 + - - -
75A VAL* 3.4 12.8 + - + +
76A VAL* 3.1 40.7 + - + +
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Residues in contact with LEU 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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32A ALA* 3.9 21.5 - - + +
33A LEU* 3.8 28.5 - - + -
36A ALA* 3.8 24.2 - - + -
41A LEU* 4.1 9.4 - - + -
69A LEU* 2.9 42.2 + - + +
70A VAL* 3.0 4.7 + - - +
72A HIS* 1.3 75.7 - - - +
74A THR* 1.3 58.5 + - - +
76A VAL* 3.6 5.7 - - + +
77A GLY 3.3 3.1 + - - -
78A VAL* 2.9 40.7 + - + +
79A LEU* 3.1 25.9 + - + -
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Residues in contact with THR 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 VAL* 2.9 21.5 + - - +
71A ARG* 3.3 12.2 - - - -
72A HIS 3.1 0.2 - - - -
73A LEU* 1.3 74.9 - - - +
75A VAL* 1.3 67.8 + - - +
77A GLY* 3.1 12.5 + - - -
79A LEU* 3.2 33.6 - - - +
80A GLU* 4.2 11.2 - - + -
81A GLY 4.4 14.8 + - - +
89A LEU* 4.5 0.9 - - - +
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Residues in contact with VAL 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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71A ARG* 3.4 17.0 - - + +
72A HIS* 3.6 12.1 - - + +
74A THR* 1.3 79.1 - - - +
76A VAL* 1.3 67.0 + - + +
77A GLY* 3.3 2.1 + - - -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASN* 5.8 0.2 - - - +
29A THR* 4.1 25.6 - - + +
33A LEU* 4.8 0.2 - - + -
72A HIS* 3.1 41.3 + - + +
73A LEU* 3.6 18.2 - - + +
74A THR 3.2 0.2 - - - -
75A VAL* 1.3 83.7 - - + +
77A GLY* 1.3 59.2 + - - +
78A VAL* 3.7 14.7 + - + +
94A LEU* 5.5 2.8 - - - +
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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