Contacts of the helix formed by residues 56 - 72 (chain A) in PDB entry 2IHU
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.0 3.4 - - - -
54A THR* 2.7 22.5 + - - -
55A ARG* 1.3 78.1 - - - +
57A GLU* 1.3 65.6 + - - +
58A PHE* 3.1 35.3 + - + +
59A THR* 3.4 10.4 + - - +
87A ASN* 3.4 44.4 + - + -
469A ASN* 4.2 10.9 + - - +
471A SER* 6.4 0.9 - - - -
472A ASP* 3.5 11.0 + - - +
1501A K 3.6 21.1 - - - -
56B HIS* 4.4 18.7 + + - -
58B PHE* 6.0 2.2 - - - +
87B ASN* 5.7 2.0 - - - -
438B PHE* 4.9 1.3 - + - -
468B SER* 3.7 19.7 - - - +
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Residues in contact with GLU 57 (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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33A VAL* 3.6 23.9 - - + +
54A THR* 4.5 0.7 - - - -
56A HIS* 1.3 73.1 + - - +
58A PHE* 1.3 66.9 + - - +
60A ALA* 3.0 18.1 + - - +
61A GLY* 3.0 10.9 + - - -
78A TRP 4.6 3.1 - - - +
79A ALA* 3.8 14.8 - - + -
84A GLY* 3.7 15.8 - - - +
87A ASN* 3.1 28.8 + - + -
88A LEU* 3.5 31.6 - - + +
438B PHE* 4.0 5.6 - - - -
600B TP9 2.6 36.4 + - - +
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Residues in contact with PHE 58 (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 HIS* 3.1 24.3 + - + +
57A GLU* 1.3 76.9 - - - +
59A THR* 1.3 60.5 + - - +
61A GLY* 3.2 2.6 + - - -
62A VAL* 3.0 49.3 + - + +
87A ASN 3.8 12.0 + - - +
90A THR* 3.5 37.2 - - + -
91A GLY* 3.9 7.1 - - - +
94A THR* 4.0 5.2 - - - -
437A SER* 3.5 23.1 - - - -
438A PHE 4.1 4.0 - - - -
439A GLY* 3.4 27.4 - - - -
440A TYR* 3.9 13.2 - + + -
443A PRO* 4.3 1.3 - - + -
469A ASN* 3.5 21.8 - - + -
56B HIS* 6.0 1.6 - - - +
87B ASN* 5.4 2.9 - - - +
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Residues in contact with THR 59 (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 THR* 3.9 11.2 - - + -
56A HIS* 3.4 7.5 + - - +
57A GLU 3.2 0.2 - - - -
58A PHE* 1.3 77.4 - - - +
60A ALA* 1.3 58.2 + - - +
63A ALA* 3.0 28.6 + - + +
443A PRO* 3.2 30.5 - - + +
446A ILE* 4.2 10.1 - - + -
469A ASN* 3.0 23.4 + - - -
472A ASP* 2.7 44.5 + - + +
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Residues in contact with ALA 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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31A PHE* 3.5 20.6 - - + +
32A GLY* 3.4 39.5 - - - +
54A THR* 3.6 12.3 + - - +
56A HIS 3.6 1.8 + - - -
57A GLU* 3.0 11.5 + - - +
59A THR* 1.3 80.8 - - - +
61A GLY* 1.3 62.7 + - - +
63A ALA* 3.5 0.6 + - - -
64A ALA* 3.2 20.8 + - - +
77A CYS* 3.8 5.6 - - + +
88A LEU* 4.6 2.0 - - + -
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Residues in contact with GLY 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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57A GLU 3.0 12.1 + - - -
58A PHE 3.2 2.4 + - - -
60A ALA* 1.3 75.8 - - - +
62A VAL* 1.3 58.0 + - - +
64A ALA* 3.6 3.3 + - - +
65A ASP* 3.1 26.2 + - - +
77A CYS* 3.9 20.0 - - - -
88A LEU* 4.1 3.9 - - - +
91A GLY* 4.1 21.8 - - - +
102A VAL* 4.6 4.6 - - - +
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Residues in contact with VAL 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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58A PHE* 3.0 45.7 + - + +
61A GLY* 1.3 73.7 - - - +
63A ALA* 1.3 60.6 + - - +
65A ASP* 3.2 6.7 + - - +
66A VAL* 2.9 29.0 + - + +
91A GLY* 4.4 1.3 - - - -
94A THR* 4.0 19.3 - - + +
440A TYR* 3.6 31.2 - - + -
443A PRO* 3.5 26.7 - - + -
444A ALA* 3.8 9.4 - - - +
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Residues in contact with ALA 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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31A PHE* 3.8 31.2 - - + -
54A THR* 5.9 0.9 - - + -
59A THR* 3.0 20.9 + - + +
60A ALA* 3.9 1.3 - - - +
62A VAL* 1.3 76.5 - - - +
64A ALA* 1.3 57.2 - - - +
67A LEU* 3.0 30.7 + - - +
443A PRO* 3.5 21.5 - - + +
446A ILE* 4.3 11.4 - - + -
447A GLY* 3.8 6.8 - - - +
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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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31A PHE* 4.0 12.0 - - + -
60A ALA 3.2 14.8 + - - +
61A GLY 3.8 4.9 - - - +
63A ALA* 1.3 76.3 - - - +
65A ASP* 1.3 58.1 + - - +
67A LEU* 4.5 0.4 - - - -
68A ALA* 2.8 32.4 + - - +
75A GLN* 3.5 14.8 - - + +
76A ALA 3.9 28.9 - - - +
77A CYS* 4.3 1.1 - - + -
102A VAL* 3.8 13.9 - - + -
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Residues in contact with ASP 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 GLY 3.1 15.4 + - - +
62A VAL* 3.2 10.6 + - - +
64A ALA* 1.3 73.9 - - - +
66A VAL* 1.3 66.2 + - - +
68A ALA* 3.2 4.2 + - - +
69A ARG* 2.8 57.0 + - - +
94A THR* 3.9 21.8 - - + +
95A SER* 3.4 16.5 + - - -
98A ASP* 4.5 0.5 - - - +
100A SER* 2.5 35.9 + - - +
102A VAL* 3.5 6.2 - - + +
440A TYR* 4.2 3.1 + - - -
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 2.9 19.8 + - + +
63A ALA 4.1 2.5 - - - +
65A ASP* 1.3 75.9 - - - +
67A LEU* 1.3 66.0 + - - +
69A ARG* 3.1 11.3 + - + +
70A ILE* 3.0 26.9 + - + +
430A LEU* 3.6 24.0 - - + -
440A TYR* 3.5 26.0 - - + +
444A ALA* 3.4 39.3 - - + +
447A GLY* 3.9 1.8 - - - -
448A ALA 3.6 11.9 - - - +
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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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29A LYS* 4.9 11.7 - - + -
31A PHE* 3.7 27.8 - - + -
63A ALA 3.0 18.8 + - - +
64A ALA 3.8 3.4 - - - +
66A VAL* 1.3 76.1 - - - +
68A ALA* 1.3 52.6 + - - +
70A ILE 4.7 0.2 - - - +
71A THR* 2.8 52.3 + - + +
75A GLN* 3.5 30.5 - - + +
447A GLY* 4.0 9.3 - - - +
450A MET* 4.3 10.8 - - + +
451A ALA* 3.8 33.4 - - + +
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Residues in contact with ALA 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 2.8 19.9 + - - +
65A ASP 3.4 5.2 - - - +
67A LEU* 1.3 74.3 - - - +
69A ARG* 1.3 59.9 + - - +
72A GLY* 2.9 30.5 + - - -
73A ARG 3.4 22.8 + - - +
75A GLN* 3.5 6.0 - - + +
100A SER* 4.2 2.9 - - - -
101A PRO* 3.7 34.7 - - + +
102A VAL* 4.5 0.2 - - + -
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Residues in contact with ARG 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 ASP* 2.8 46.7 + - - -
66A VAL* 3.1 17.9 + - + +
68A ALA* 1.3 79.1 - - - +
70A ILE* 1.3 66.2 + - + +
72A GLY* 3.6 6.1 + - - -
98A ASP* 3.0 37.4 + - - +
99A ARG 3.5 11.9 + - - +
100A SER* 3.9 3.9 - - - -
101A PRO* 5.5 1.3 - - - -
225A ALA* 5.8 0.4 - - - +
229A ARG* 5.9 5.4 - - + +
252A ILE* 3.7 20.6 - - - +
427A PHE* 3.6 52.7 - - + -
430A LEU* 4.6 10.3 - - - +
440A TYR* 4.2 7.2 + - - -
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Residues in contact with ILE 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 VAL* 3.0 15.6 + - + +
69A ARG* 1.3 79.4 - - + +
71A THR* 1.3 61.9 + - + +
72A GLY 3.6 0.2 + - - -
427A PHE* 4.4 16.2 - - + -
430A LEU* 3.9 19.7 - - + -
448A ALA* 3.7 31.4 - - + -
451A ALA* 3.6 26.7 - - + +
452A ARG* 3.6 42.8 - - + +
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Residues in contact with THR 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 LEU* 2.8 46.0 + - + +
70A ILE* 1.3 76.3 - - + +
72A GLY* 1.3 60.8 + - - +
73A ARG* 3.2 58.8 + - - +
75A GLN* 3.2 14.3 + - - +
451A ALA* 4.5 9.9 - - + +
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Residues in contact with GLY 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 ALA 2.9 14.8 + - - -
69A ARG 3.6 5.9 + - - -
70A ILE 3.4 3.0 + - - -
71A THR* 1.3 77.4 - - - +
73A ARG* 1.3 59.9 + - - +
101A PRO* 5.1 4.0 - - - -
157A MET* 4.2 18.9 - - - +
191A PRO 5.1 0.9 - - - +
192A ALA 4.3 11.3 - - - +
193A LYS* 5.5 0.3 - - - -
194A PRO* 5.9 0.9 - - - +
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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