Contacts of the helix formed by residues 29 - 50 (chain A) in PDB entry 1HK8
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 VAL 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASP* 4.2 27.9 + - + +
27A SER 3.3 1.0 - - - +
28A ARG* 1.3 78.8 - - - +
30A PHE* 1.3 64.7 + - - +
31A PRO* 3.4 20.4 - - + -
32A THR* 3.2 21.3 + - - +
33A GLN* 3.1 17.3 + - - +
186A PHE* 4.8 14.8 - - + -
190A GLY 5.1 1.1 - - - +
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG 3.7 4.8 + - - -
29A VAL* 1.3 70.9 - - - +
31A PRO* 1.3 72.6 - - + +
33A GLN* 3.0 19.8 + - + +
34A ARG* 3.0 22.6 + - + +
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Residues in contact with PRO 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.4 17.7 - - + -
30A PHE* 1.3 96.9 - - + +
32A THR* 1.3 54.3 + - - +
34A ARG* 3.7 9.4 - - + +
35A ASP* 3.0 28.6 + - - +
186A PHE* 4.5 13.7 - - + -
187A SER 5.5 0.4 - - - +
188A SER 4.5 6.5 - - - +
189A ASN 4.2 2.8 - - - +
190A GLY* 3.7 23.8 - - - +
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP 3.6 19.6 + - - +
27A SER* 3.9 29.6 - - - +
29A VAL* 3.2 18.3 + - - +
31A PRO* 1.3 78.2 - - - +
33A GLN* 1.3 58.9 + - - +
35A ASP* 3.3 4.1 + - + +
36A LEU* 2.9 37.0 + - + +
189A ASN 4.1 11.5 + - - +
190A GLY 4.0 11.6 + - - -
191A GLN* 5.3 3.8 - - + +
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER 3.5 18.9 - - - +
28A ARG* 4.0 25.3 + - - +
29A VAL 3.1 14.0 + - - +
30A PHE* 3.0 14.1 + - + +
32A THR* 1.3 71.9 - - - +
34A ARG* 1.3 66.7 + - + +
36A LEU* 3.3 15.7 + - - +
37A MET* 3.1 33.3 + - + +
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Residues in contact with ARG 34 (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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30A PHE* 3.0 20.3 + - + +
31A PRO* 3.7 10.3 - - + +
33A GLN* 1.3 76.6 - - + +
35A ASP* 1.3 59.6 - - - +
37A MET* 3.1 32.6 + - - +
38A ALA* 3.2 13.2 + - - +
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Residues in contact with ASP 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO 3.0 18.8 + - - +
32A THR* 3.6 6.3 - - + +
33A GLN 3.2 0.2 - - - -
34A ARG* 1.3 74.3 - - - +
36A LEU* 1.3 67.1 + - - +
38A ALA* 3.2 8.6 + - - +
39A GLY* 2.8 26.9 + - - -
69A ASP* 5.2 3.6 - - - +
70A TYR* 3.3 28.3 + - - -
188A SER* 4.9 3.8 + - - +
189A ASN* 3.4 33.1 - - - +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 4.9 9.9 - - - +
32A THR* 2.9 25.1 + - + +
33A GLN* 3.6 21.5 - - - +
35A ASP* 1.3 82.0 - - - +
37A MET* 1.3 62.8 + - - +
39A GLY* 3.7 3.1 - - - +
40A ILE* 3.0 35.6 + - + +
69A ASP* 6.1 0.9 - - - +
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Residues in contact with MET 37 (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 GLN* 3.1 21.7 + - + +
34A ARG* 3.4 28.7 - - - +
35A ASP 3.1 0.4 - - - -
36A LEU* 1.3 77.6 - - + +
38A ALA* 1.3 60.1 + - - +
40A ILE* 3.4 6.3 + - - +
41A VAL* 3.1 29.2 + - + +
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Residues in contact with ALA 38 (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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34A ARG 3.2 8.4 + - - +
35A ASP* 3.2 12.6 + - - +
37A MET* 1.3 74.9 - - - +
39A GLY* 1.3 60.3 + - - +
41A VAL* 3.4 7.7 + - - +
42A SER* 2.9 36.6 + - - +
69A ASP 4.6 0.9 - - - -
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Residues in contact with GLY 39 (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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35A ASP* 2.8 17.4 + - - -
36A LEU* 3.3 5.1 + - - -
37A MET 3.3 0.2 - - - -
38A ALA* 1.3 77.4 - - - +
40A ILE* 1.3 58.9 + - - +
42A SER* 3.4 2.1 + - - -
43A LYS* 3.0 33.0 + - - +
69A ASP* 3.6 29.8 - - - +
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Residues in contact with ILE 40 (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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36A LEU* 3.0 26.7 + - + +
37A MET* 3.6 7.2 - - - +
38A ALA 3.3 0.2 - - - -
39A GLY* 1.3 73.7 - - - +
41A VAL* 1.3 70.6 + - + +
42A SER 3.1 1.3 - - - -
43A LYS* 3.3 30.3 + - + +
44A HIS* 3.2 22.5 + - + +
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Residues in contact with VAL 41 (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 MET* 3.1 18.0 + - + +
38A ALA* 3.8 7.9 - - - +
40A ILE* 1.3 80.0 - - + +
42A SER* 1.3 57.4 + - - +
44A HIS* 3.4 8.2 + - + +
45A ILE* 3.1 44.8 + - + +
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 2.9 20.8 + - - +
39A GLY 3.7 0.7 - - - -
40A ILE 3.1 0.4 - - - -
41A VAL* 1.3 78.2 - - - +
43A LYS* 1.3 58.8 + - - +
45A ILE* 3.4 1.7 + - - +
46A ALA* 3.0 27.9 + - - +
68A ILE 3.9 3.8 - - - +
69A ASP 3.2 31.1 + - - -
70A TYR* 4.4 4.0 + - - -
73A ALA* 3.7 27.4 - - - +
74A LEU* 5.4 6.2 - - - +
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLY 3.0 20.9 + - - +
40A ILE* 3.3 27.1 + - + +
42A SER* 1.3 76.6 - - - +
44A HIS* 1.3 59.1 + - - +
46A ALA* 3.4 6.1 + - - +
47A LYS* 3.2 35.8 + - - +
68A ILE* 4.1 29.3 + - + +
69A ASP* 3.9 19.7 - - - +
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Residues in contact with HIS 44 (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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40A ILE* 3.2 13.8 + - + +
41A VAL* 3.5 12.1 - - + +
42A SER 3.2 0.2 - - - -
43A LYS* 1.3 73.8 - - - +
45A ILE* 1.3 70.7 + - - +
47A LYS* 3.2 24.6 + - + +
48A ASN* 3.5 27.3 + - - +
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Residues in contact with ILE 45 (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 VAL* 3.1 34.1 + - + +
42A SER* 3.7 4.7 - - - +
43A LYS 3.3 0.2 - - - -
44A HIS* 1.3 80.8 - - - +
46A ALA* 1.3 61.1 + - - +
48A ASN* 3.1 19.3 + - + +
49A MET* 3.1 30.9 + - + +
73A ALA* 3.5 29.2 - - + +
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Residues in contact with ALA 46 (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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42A SER 3.0 16.9 + - - +
43A LYS 3.5 6.5 - - - +
44A HIS 3.3 0.2 - - - -
45A ILE* 1.3 78.4 - - - +
47A LYS* 1.3 56.8 + - - +
49A MET* 4.3 7.0 - - - +
50A VAL* 3.0 37.2 + - + +
55A MET* 4.4 4.0 - - + +
68A ILE* 3.9 35.7 - - + +
72A PRO* 4.0 13.7 - - + -
73A ALA* 4.8 0.9 - - - +
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Residues in contact with LYS 47 (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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43A LYS* 3.2 25.4 + - - +
44A HIS* 3.3 16.4 - - + +
45A ILE 3.2 0.2 - - - -
46A ALA* 1.3 78.0 - - - +
48A ASN* 1.3 63.6 + - - +
50A VAL 4.0 9.2 - - - +
55A MET* 4.4 26.6 - - + +
59A GLU* 3.7 23.7 + - - +
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Residues in contact with ASN 48 (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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44A HIS* 3.5 32.1 + - - +
45A ILE* 3.1 12.3 + - + +
47A LYS* 1.3 84.2 + - - +
49A MET* 1.3 59.8 + - + +
50A VAL 3.8 0.7 - - - -
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Residues in contact with MET 49 (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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45A ILE* 3.1 36.7 + - + +
46A ALA 3.2 3.1 + - - +
48A ASN* 1.3 80.3 - - + +
50A VAL* 1.3 63.3 + - - +
51A PRO* 3.7 6.6 - - - +
72A PRO* 3.2 50.9 - - + +
73A ALA* 4.0 2.7 - - - +
354A CYS* 4.5 5.7 - - - -
358A SER* 4.4 12.6 - - - -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 3.0 18.5 + - - +
47A LYS 4.0 12.0 - - - +
48A ASN 5.0 0.3 - - - -
49A MET* 1.3 79.9 + - - +
51A PRO* 1.3 79.4 - - + +
52A SER* 3.4 2.3 + - - -
54A ILE* 3.5 28.0 - - + -
55A MET* 3.4 35.8 - - + +
65A VAL* 6.5 0.2 - - + -
68A ILE* 4.7 1.6 - - + -
72A PRO* 3.9 27.6 - - + -
354A CYS* 4.2 11.2 - - - -
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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
------------------------------------------------------------
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