Contacts of the helix formed by residues 57 - 67 (chain A) in PDB entry 1HS7
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 SER 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LYS* 5.2 1.4 + - - -
55A ARG 2.5 20.0 + - - -
56A ASP* 1.3 75.0 - - - +
58A LYS* 1.3 56.1 + - - +
59A GLU* 4.2 9.8 - - - +
60A LEU* 2.6 37.8 + - - +
61A ARG* 2.9 16.3 - - - +
118A LEU* 3.6 2.4 - - - +
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Residues in contact with LYS 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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57A SER* 1.3 70.9 - - - +
59A GLU* 1.3 52.2 + - - +
61A ARG* 3.2 14.5 - - - +
62A TYR* 2.7 62.9 + - + +
118A LEU* 3.6 22.0 - - + +
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Residues in contact with GLU 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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57A SER* 3.0 7.3 - - - +
58A LYS* 1.3 79.6 - - + +
60A LEU* 1.3 53.5 + - - +
62A TYR* 3.7 5.5 - - - +
63A LYS* 2.7 36.7 + - - +
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Residues in contact with LEU 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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47A GLU* 3.5 23.3 - - + +
50A LYS* 3.1 38.1 - - + +
51A ILE* 3.6 23.6 - - + -
55A ARG 4.0 11.7 - - - +
56A ASP* 4.2 6.7 - - - -
57A SER* 2.6 28.1 + - - +
59A GLU* 1.3 68.5 - - - +
61A ARG* 1.3 57.1 + - - +
62A TYR 3.0 1.1 - - - -
63A LYS* 3.0 8.4 + - - +
64A ILE* 2.6 60.3 + - + -
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Residues in contact with ARG 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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51A ILE* 4.3 14.4 - - + +
52A GLY 5.8 0.6 - - - +
56A ASP* 5.4 2.0 - - - +
57A SER 2.9 30.7 - - - +
58A LYS* 3.2 21.2 - - + +
60A LEU* 1.3 80.9 - - - +
62A TYR* 1.3 59.3 + - + +
64A ILE* 3.5 7.4 - - - +
65A GLU* 2.9 34.9 + - + +
109A TYR* 4.1 12.3 - - - +
113A LYS* 3.3 54.1 + - - +
116A PHE 4.4 7.7 + - - -
117A PRO* 5.3 1.6 - - - +
118A LEU* 3.2 29.7 - - - +
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Residues in contact with TYR 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 LYS* 2.7 51.5 + - + +
59A GLU* 3.7 7.0 - - + +
61A ARG* 1.3 78.1 - - + +
63A LYS* 1.3 55.1 + - - +
65A GLU* 5.1 0.2 - - - -
66A THR* 2.4 67.8 + - + +
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Residues in contact with LYS 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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46A LYS* 4.5 8.5 - - - +
47A GLU* 3.0 49.4 + - - +
59A GLU 2.7 23.3 + - - +
60A LEU* 3.5 7.2 - - - +
62A TYR* 1.3 73.0 - - - +
64A ILE* 1.3 51.0 + - - +
66A THR* 3.7 6.1 - - - -
67A GLU* 2.7 45.4 + - - +
68A LEU* 2.7 53.3 + - - +
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Residues in contact with ILE 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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44A LEU* 4.4 2.0 - - + -
47A GLU* 3.4 32.1 - - + -
48A CYS* 4.0 6.5 - - - +
51A ILE* 3.9 8.3 - - + -
60A LEU* 2.6 31.2 + - + +
61A ARG 3.5 2.9 - - - +
63A LYS* 1.3 73.8 - - - +
65A GLU* 1.3 62.5 + - + +
68A LEU* 3.0 31.2 + - + -
69A ILE* 2.7 38.3 + - + +
70A PRO* 3.2 0.2 - - - +
109A TYR* 2.9 52.3 - - + +
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Residues in contact with GLU 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 ARG 2.9 12.2 + - - +
62A TYR* 4.3 0.4 - - - +
64A ILE* 1.3 80.9 - - + +
66A THR* 1.3 62.0 + - + +
69A ILE* 4.4 11.7 - - + +
70A PRO* 2.9 24.4 - - - +
109A TYR* 3.3 19.4 + - - +
110A ASN* 3.7 10.2 + - - +
113A LYS* 3.0 26.8 + - - +
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Residues in contact with THR 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 TYR* 2.4 68.5 + - + +
63A LYS* 3.7 3.8 - - - -
65A GLU* 1.3 77.0 - - + +
67A GLU* 1.3 58.1 + - - +
70A PRO* 3.2 11.7 - - - +
71A ASN* 5.5 0.3 - - - +
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Residues in contact with GLU 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 LYS* 2.7 56.6 + - + +
66A THR* 1.3 80.1 - - - +
68A LEU* 1.3 68.6 + - + +
70A PRO* 3.1 4.2 - - - +
71A ASN* 2.7 46.0 + - - +
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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