Contacts of the helix formed by residues 59 - 74 (chain A) in PDB entry 1H6H
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 TYR 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE 4.5 0.4 + - - -
41A PHE* 4.1 16.8 - - + -
58A ARG* 1.3 73.7 - - - +
60A ARG* 1.3 62.4 + - - +
62A PHE* 2.9 24.8 + - + +
63A HIS* 3.0 41.5 + + + -
89A LEU* 4.0 15.1 - - + +
90A PRO* 2.7 32.3 + - + -
91A ALA* 3.3 11.5 - - - -
92A LYS* 3.3 8.2 + - + -
105A ARG* 3.5 48.7 - - - +
109A LEU* 4.9 9.0 - - + -
150A PIB 3.3 43.6 + - - +
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Residues in contact with ARG 60 (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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58A ARG* 3.2 34.5 + - - +
59A TYR* 1.3 75.7 - - - +
61A GLN* 1.3 59.9 + - + +
63A HIS* 3.8 4.9 - - + +
64A ALA* 3.1 27.7 + - - +
150A PIB 2.8 76.8 + - - +
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Residues in contact with GLN 61 (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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56A TYR 4.1 3.6 + - - +
57A ARG* 3.2 23.6 - - - +
58A ARG* 2.9 47.3 + - + +
60A ARG* 1.3 77.3 - - + +
62A PHE* 1.3 66.2 + - - +
64A ALA* 3.5 6.0 + - - +
65A LEU* 3.1 21.8 + - - +
132A PHE* 4.0 17.1 - - + -
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Residues in contact with PHE 62 (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 ILE* 5.7 0.4 - - + -
41A PHE* 4.5 4.0 - + + -
43A ILE* 3.8 24.0 - - + -
57A ARG* 4.0 18.6 - - + -
58A ARG 3.5 17.2 + - - -
59A TYR* 2.9 16.7 + - + +
61A GLN* 1.3 79.6 - - - +
63A HIS* 1.3 57.3 + - - +
65A LEU* 3.2 6.2 + - + +
66A GLN* 3.0 28.6 + - - +
89A LEU* 3.8 14.3 - - + +
109A LEU* 4.0 39.3 - - + -
112A TYR* 4.1 19.9 + + - -
113A MET* 3.9 27.6 - - + -
132A PHE* 3.7 29.6 - + - -
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Residues in contact with HIS 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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59A TYR* 3.0 44.6 + - + +
60A ARG* 3.5 7.4 + - - +
61A GLN 3.3 0.2 - - - -
62A PHE* 1.3 77.9 - - - +
64A ALA* 1.3 62.5 + - - +
66A GLN* 3.3 3.2 + - + +
67A SER* 3.0 43.2 + - - -
89A LEU* 3.6 13.6 - - + +
91A ALA* 6.0 0.4 - - - -
92A LYS* 3.5 39.3 + - + +
150A PIB 4.9 1.6 - - - +
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Residues in contact with ALA 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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60A ARG 3.1 17.8 + - - +
61A GLN* 3.9 6.1 - - - +
62A PHE 3.3 0.2 - - - -
63A HIS* 1.3 76.5 - - - +
65A LEU* 1.3 63.9 + - - +
67A SER* 3.5 7.9 + - - -
68A LYS* 3.4 34.4 + - - +
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Residues in contact with LEU 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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61A GLN 3.1 15.2 + - - +
62A PHE* 3.6 7.6 - - - +
63A HIS 3.2 0.2 - - - -
64A ALA* 1.3 74.8 - - - +
66A GLN* 1.3 67.6 + - - +
68A LYS* 3.0 21.0 + - + +
69A LEU* 3.1 23.7 + - + +
112A TYR* 4.6 8.3 - - + +
116A LEU* 4.5 21.3 - - + -
128A ASP* 3.9 38.6 - - + +
129A VAL* 4.1 13.9 - - + +
132A PHE* 3.8 37.9 - - + -
133A PHE* 5.3 0.2 - - + -
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Residues in contact with GLN 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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62A PHE 3.0 15.8 + - - +
63A HIS* 3.3 5.4 + - + +
65A LEU* 1.3 77.5 - - - +
67A SER* 1.3 62.6 + - - +
69A LEU* 3.2 15.7 + - - +
70A GLU* 2.9 57.5 + - - +
86A LEU* 4.5 10.8 - - - +
87A PRO* 2.9 26.4 + - - +
88A THR* 4.4 1.4 - - - +
89A LEU* 4.1 24.8 - - + +
112A TYR* 2.7 36.2 + - - +
116A LEU* 5.7 0.2 - - - +
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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
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63A HIS* 3.0 35.6 + - - -
64A ALA* 3.7 9.3 - - - -
65A LEU 3.2 0.2 - - - -
66A GLN* 1.3 78.0 - - - +
68A LYS* 1.3 61.9 + - - +
70A GLU* 3.5 11.9 + - - +
71A GLU* 3.3 36.0 + - - +
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Residues in contact with LYS 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 ALA* 3.4 23.7 + - - +
65A LEU* 3.0 13.6 + - + +
67A SER* 1.3 75.6 - - - +
69A LEU* 1.3 66.7 + - + +
71A GLU* 3.2 10.9 + - - +
72A ARG* 3.1 51.5 + - - +
128A ASP* 3.5 38.0 + - + +
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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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65A LEU* 3.1 28.0 + - + +
66A GLN* 3.2 21.7 + - - +
68A LYS* 1.3 77.5 - - + +
70A GLU* 1.3 58.6 + - - +
72A ARG* 4.7 0.9 - - - +
73A PHE* 2.7 56.7 + - + +
86A LEU* 3.5 22.8 - - + +
112A TYR* 4.3 1.8 - - - +
116A LEU* 3.9 28.0 - - + -
123A VAL* 4.7 2.5 - - + -
126A ASP* 4.4 9.6 - - - +
129A VAL* 3.7 26.2 - - + -
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Residues in contact with GLU 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 GLN* 2.9 48.4 + - - +
67A SER* 3.9 11.5 + - - +
68A LYS 3.3 0.2 - - - -
69A LEU* 1.3 75.8 - - - +
71A GLU* 1.3 59.8 + - + +
74A GLY* 2.9 27.5 + - - +
75A PRO* 5.1 3.1 - - + +
76A ASP* 5.1 1.9 + - - +
77A SER* 3.8 5.4 + - - -
86A LEU* 3.9 13.0 - - + -
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Residues in contact with GLU 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* 3.3 23.3 + - - +
68A LYS* 3.2 12.2 + - - +
70A GLU* 1.3 77.6 - - + +
72A ARG* 1.3 62.5 + - + +
76A ASP 5.8 0.9 - - - -
77A SER* 3.1 21.7 + - - +
78A LYS 4.9 0.2 + - - -
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Residues in contact with ARG 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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68A LYS* 3.1 39.7 + - - +
69A LEU* 5.1 1.2 - - - +
71A GLU* 1.3 79.6 - - + +
73A PHE* 1.3 84.7 + - + +
77A SER* 2.9 16.8 + - - -
79A SER* 4.4 10.5 + - - -
82A LEU* 4.5 4.7 - - - +
83A ALA 5.3 0.3 + - - -
126A ASP* 2.9 33.9 + - - -
127A GLU* 5.4 0.4 - - - +
128A ASP* 2.8 32.5 + - - +
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Residues in contact with PHE 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 LEU* 2.7 41.9 + - + +
72A ARG* 1.3 94.7 - - + +
74A GLY* 1.3 62.6 + - - +
77A SER* 4.1 1.3 - - - -
82A LEU* 3.4 34.1 - - + +
83A ALA* 3.5 5.7 - - - +
84A CYS* 3.3 32.8 + - - +
86A LEU* 4.2 14.4 - - + -
122A TRP* 3.7 36.1 - + - -
123A VAL* 4.0 20.2 - - + -
126A ASP* 3.8 23.8 - - - -
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Residues in contact with GLY 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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69A LEU 3.6 2.0 + - - -
70A GLU* 2.9 22.7 + - - -
73A PHE* 1.3 81.6 - - - +
75A PRO* 1.3 70.0 - - - +
76A ASP 3.4 2.5 - - - -
77A SER* 2.9 23.5 + - - +
83A ALA* 4.8 7.7 - - - +
84A CYS 5.0 2.2 - - - -
86A LEU* 4.1 7.6 - - - +
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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