Contacts of the helix formed by residues 51 - 60 (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 PRO 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A MET 3.7 7.4 - - - +
50A VAL* 1.3 88.2 - - + +
52A SER* 1.3 65.4 + - - +
53A PHE* 3.3 27.1 - - + -
54A ILE* 3.0 25.8 + - + +
55A MET 3.2 8.1 + - - -
350A GLU* 6.4 0.2 - - + -
354A CYS* 3.7 18.4 - - + -
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Residues in contact with SER 52 (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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50A VAL 3.4 4.3 + - - -
51A PRO* 1.3 70.8 - - - +
53A PHE* 1.3 57.7 + - - +
55A MET* 3.3 6.9 + - - +
56A LYS* 2.8 46.5 + - - +
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Residues in contact with PHE 53 (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 PRO* 3.2 25.3 + - + -
52A SER* 1.3 78.9 - - - +
54A ILE* 1.3 68.0 + - + +
56A LYS* 4.1 5.8 - - - +
57A ALA* 3.2 27.5 + - - +
347A LEU* 3.5 29.9 - - + +
350A GLU* 3.6 30.7 - - + -
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Residues in contact with ILE 54 (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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50A VAL* 3.5 17.5 - - + -
51A PRO* 3.0 27.9 + - + +
53A PHE* 1.3 106.9 - - + +
55A MET* 1.3 64.5 + - + +
57A ALA* 3.3 7.0 + - - +
58A HIS* 3.1 20.7 + - - +
63A ILE* 4.1 3.9 - - + +
65A VAL* 4.3 12.8 - - + -
347A LEU* 4.2 8.5 - - + -
350A GLU* 3.6 32.1 - - + +
351A ALA* 3.9 24.7 - - + +
354A CYS* 4.4 3.6 - - + -
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Residues in contact with MET 55 (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 ALA* 4.4 6.5 - - + +
47A LYS* 4.4 31.2 - - + +
50A VAL* 3.4 50.3 - - + +
51A PRO 3.2 5.4 + - - +
52A SER* 3.6 10.1 - - - +
54A ILE* 1.3 82.3 - - + +
56A LYS* 1.3 64.6 + - + +
58A HIS* 3.0 19.6 + - + +
59A GLU* 2.9 37.4 + - - +
65A VAL* 5.3 7.4 - - + -
68A ILE* 3.7 27.4 - - + -
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Residues in contact with LYS 56 (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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52A SER* 2.8 36.1 + - - +
53A PHE* 4.1 7.4 - - - +
55A MET* 1.3 72.9 - - + +
57A ALA* 1.3 62.5 + - - +
59A GLU* 3.4 22.1 + - + +
60A SER* 3.1 25.9 + - - -
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Residues in contact with ALA 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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53A PHE 3.2 17.8 + - - +
54A ILE 3.6 5.8 - - - +
55A MET 3.2 0.4 - - - -
56A LYS* 1.3 80.4 - - - +
58A HIS* 1.3 56.0 + - - +
60A SER* 3.3 5.7 + - - -
61A GLY 3.2 4.7 + - - -
62A ILE* 3.0 39.7 + - + +
63A ILE* 3.4 9.9 + - + -
347A LEU* 3.8 28.0 - - + -
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Residues in contact with HIS 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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54A ILE 3.1 11.7 + - - +
55A MET* 3.0 23.1 + - + +
57A ALA* 1.3 73.0 - - - +
59A GLU* 1.3 78.1 + - - +
60A SER 3.1 2.5 + - - -
61A GLY 3.3 4.2 + - - -
63A ILE* 3.7 9.1 - - + +
64A HIS* 3.6 28.4 - + - -
65A VAL* 3.0 53.9 + - + +
68A ILE* 4.7 15.2 - - + +
451A ARG* 2.9 38.7 + - - -
1588A DGT 5.7 0.8 + - - -
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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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47A LYS* 3.7 28.4 + - - +
55A MET* 2.9 33.2 + - - +
56A LYS* 3.4 22.2 + - + +
58A HIS* 1.3 87.6 - - - +
60A SER* 1.3 59.9 + - - +
61A GLY 3.6 0.2 + - - -
451A ARG* 4.0 7.5 + - - +
455A LEU* 3.4 22.2 - - - +
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Residues in contact with SER 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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56A LYS 3.1 13.2 + - - -
57A ALA* 3.3 5.5 + - - -
58A HIS 3.1 0.2 - - - -
59A GLU* 1.3 77.7 - - - +
61A GLY* 1.3 56.6 + - - +
62A ILE* 3.2 25.5 - - - +
321A ARG* 3.0 34.0 + - - -
455A LEU* 3.8 14.1 - - - +
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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