Contacts of the helix formed by residues 35 - 49 (chain A) in PDB entry 4HX8
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 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ALA* 4.5 0.7 - - - -
34A VAL* 1.3 75.1 - - - +
36A PRO* 1.3 83.8 - - + +
37A SER* 2.9 34.3 - - - +
38A SER* 2.9 33.3 + - - +
39A VAL* 3.3 5.7 + - - +
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Residues in contact with PRO 36 (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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25A VAL* 4.2 9.2 - - + +
26A SER* 6.2 1.3 - - - -
29A ALA* 4.0 19.5 - - + -
34A VAL 3.6 4.0 - - - +
35A HIS* 1.3 102.9 - - + +
37A SER* 1.3 54.9 + - - +
39A VAL* 3.2 7.1 + - + +
40A THR* 3.0 31.2 + - - -
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Residues in contact with SER 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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35A HIS* 2.9 30.3 - - - +
36A PRO* 1.3 76.5 - - - +
38A SER* 1.3 67.0 + - - +
40A THR* 3.4 8.5 + - - -
41A LYS* 3.1 23.9 + - - +
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Residues in contact with SER 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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9A TYR* 3.3 12.6 + - - -
34A VAL* 4.4 8.4 - - - +
35A HIS* 2.9 24.3 + - - +
37A SER* 1.3 80.6 + - - +
39A VAL* 1.3 61.3 + - - +
41A LYS* 3.4 9.3 + - - +
42A MET* 3.1 19.9 + - - +
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Residues in contact with VAL 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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9A TYR* 3.1 18.3 + - + +
25A VAL* 3.4 33.9 - - + +
28A ILE* 4.0 17.7 - - + -
29A ALA* 3.7 37.9 - - + +
34A VAL* 3.9 4.9 - - + -
35A HIS 3.8 7.4 - - - +
36A PRO 3.2 7.4 - - - +
38A SER* 1.3 76.7 - - - +
40A THR* 1.3 55.4 + - - +
42A MET* 3.3 3.3 + - - +
43A VAL* 2.9 43.7 + - + +
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Residues in contact with THR 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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25A VAL* 4.3 13.8 - - - +
36A PRO 3.0 14.2 + - - -
37A SER* 3.6 11.6 - - - +
39A VAL* 1.3 74.3 - - - +
41A LYS* 1.3 67.2 + - - +
43A VAL* 3.3 5.7 + - - +
44A GLN* 3.1 47.1 + - + +
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Residues in contact with LYS 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 SER 3.1 14.0 + - - +
38A SER* 3.7 10.5 - - - +
39A VAL 3.4 0.2 - - - -
40A THR* 1.3 78.3 - - - +
42A MET* 1.3 62.6 + - - +
44A GLN* 3.5 6.2 + - - +
45A LYS* 3.4 17.7 + - - +
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Residues in contact with MET 42 (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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5A SER* 4.1 9.9 - - - +
6A MET* 3.6 48.2 - - + +
9A TYR* 3.5 51.4 - - + -
38A SER 3.1 10.9 + - - +
39A VAL 3.3 0.9 + - - +
41A LYS* 1.3 77.6 - - - +
43A VAL* 1.3 57.7 + - - +
45A LYS* 3.3 17.0 + - + +
46A LEU* 2.9 43.4 + - + +
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Residues in contact with VAL 43 (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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9A TYR* 5.3 2.2 - - + -
13A ILE* 5.0 5.8 - - + -
25A VAL* 4.4 5.6 - - + -
28A ILE* 5.0 0.2 - - + -
39A VAL* 2.9 38.0 + - + +
40A THR* 3.3 7.8 + - - +
42A MET* 1.3 75.3 - - - +
44A GLN* 1.3 65.4 + - - +
46A LEU* 3.8 7.7 - - + +
47A ASP* 2.8 27.7 + - - +
52A LEU* 4.1 10.8 - - + -
54A TYR* 3.9 42.4 - - + -
60A LEU* 4.0 19.5 - - + -
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Residues in contact with GLN 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 THR* 3.1 32.6 + - + +
41A LYS* 3.9 6.7 - - - +
42A MET 3.2 0.6 - - - -
43A VAL* 1.3 81.8 - - - +
45A LYS* 1.3 59.5 + - - +
47A ASP* 3.8 8.7 - - - +
48A LYS* 2.9 36.4 + - - +
54A TYR* 4.2 26.1 - - - -
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Residues in contact with LYS 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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6A MET* 3.4 35.4 - - + -
41A LYS 3.4 10.4 + - - +
42A MET* 3.3 23.1 + - + +
44A GLN* 1.3 78.2 - - - +
46A LEU* 1.3 57.0 + - - +
48A LYS* 3.2 14.9 - - + +
49A ASP* 2.8 49.9 + - - +
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Residues in contact with LEU 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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6A MET* 3.6 29.4 - - + -
9A TYR* 4.1 10.5 - - + -
10A ILE* 4.3 16.4 - - + -
13A ILE* 4.1 13.5 - - + -
42A MET* 2.9 46.6 + - + +
43A VAL* 3.8 2.2 - - + +
45A LYS* 1.3 73.5 - - - +
47A ASP* 1.3 56.2 + - - +
49A ASP 3.5 0.5 + - - -
50A GLU 2.9 7.1 + - - -
51A TYR* 2.7 48.1 + - + -
52A LEU* 3.4 34.6 + - + -
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Residues in contact with ASP 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 VAL 2.8 23.0 + - - +
44A GLN* 3.9 11.0 - - - +
46A LEU* 1.3 71.0 - - - +
48A LYS* 1.3 66.7 + - - +
50A GLU* 3.0 14.7 + - - +
52A LEU* 3.5 15.8 - - + +
53A ILE* 3.5 6.7 - - - +
54A TYR* 2.7 42.3 + - + +
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Residues in contact with LYS 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 GLN 2.9 20.4 + - - +
45A LYS* 3.2 20.4 - - + +
47A ASP* 1.3 75.3 - - - +
49A ASP* 1.3 79.7 + - - +
50A GLU* 3.2 3.3 + - - +
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Residues in contact with ASP 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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6A MET* 3.9 7.6 - - - +
45A LYS* 2.8 41.2 + - - +
48A LYS* 1.3 94.8 - - - +
50A GLU* 1.3 69.6 + - - +
51A TYR* 3.3 23.7 + - + -
65A LYS* 3.4 14.6 + - - -
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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