Contacts of the helix formed by residues 319 - 325 (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 LEU 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A LEU* 3.1 42.8 + - + +
318A ASN* 1.3 69.4 - - - +
320A PRO* 1.3 77.9 - - + +
322A ILE* 3.0 28.1 + - + +
323A ALA 3.4 2.9 + - - -
341A PHE* 5.1 0.7 - - + -
401A TYR* 3.9 27.4 - - + -
402A ILE 3.4 11.3 + - - +
404A ILE* 4.3 10.3 - - + -
407A LEU* 3.7 33.9 - - + +
419A ILE* 4.5 13.5 - - + -
420A LEU* 4.5 9.4 - - + -
423A MET* 4.2 12.3 - - + -
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Residues in contact with PRO 320 (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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318A ASN* 3.5 6.1 - - - +
319A LEU* 1.3 89.8 - - + +
321A ARG* 1.3 57.5 + - - +
323A ALA* 3.0 7.1 + - + +
324A LEU* 2.8 31.1 + - + +
402A ILE* 3.2 16.8 - - + +
403A GLY* 3.5 20.6 - - - +
406A GLU* 4.0 12.3 - - + -
407A LEU* 4.4 3.8 - - + +
410A LEU* 3.6 19.2 - - + +
466A VAL* 4.9 0.2 - - + -
472A TYR* 3.7 38.1 - - + +
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Residues in contact with ARG 321 (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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60A SER* 3.0 33.5 + - - -
61A GLY 4.4 3.2 - - - +
62A ILE* 3.8 27.8 - - + +
318A ASN* 3.3 33.2 + - + +
319A LEU 3.2 1.2 - - - -
320A PRO* 1.3 76.9 - - - +
322A ILE* 1.3 63.7 + - - +
324A LEU* 4.2 4.3 - - - -
325A ASP* 3.0 54.9 + - - +
344A ARG* 3.7 1.3 - - - +
455A LEU 4.1 10.5 + - - -
456A ASP* 2.9 30.9 + - - +
459A LYS* 4.1 21.6 - - - +
460A TYR* 4.1 12.6 - - - -
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Residues in contact with ILE 322 (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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317A LEU* 3.6 34.5 - - + -
318A ASN 3.3 14.8 - - - +
319A LEU* 3.0 18.1 + - + +
321A ARG* 1.3 78.0 - - - +
323A ALA* 1.3 61.8 + - - +
325A ASP* 3.5 3.5 + - - +
326A SER* 3.3 19.8 + - - -
337A PHE* 3.7 26.2 - - + +
340A LEU* 3.8 10.4 - - + +
341A PHE* 4.0 37.7 - - + +
344A ARG* 3.4 24.7 - - + +
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Residues in contact with ALA 323 (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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319A LEU 3.4 0.8 + - - -
320A PRO 3.0 8.6 + - - +
322A ILE* 1.3 77.7 - - - +
324A LEU* 1.3 66.4 + - - +
326A SER* 2.8 25.3 + - - -
327A TYR* 3.2 15.2 - - - -
332A PHE* 4.2 7.9 - - + -
337A PHE* 3.8 8.7 - - + -
407A LEU* 3.9 20.0 - - + -
410A LEU* 3.7 27.1 - - + -
411A VAL* 4.4 1.3 - - + -
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Residues in contact with LEU 324 (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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320A PRO 2.8 23.2 + - - +
321A ARG* 3.9 4.5 - - - +
323A ALA* 1.3 71.4 - - - +
325A ASP* 1.3 57.5 + - - +
326A SER 3.1 0.2 - - - -
327A TYR* 3.2 29.8 + - + +
410A LEU* 3.6 29.2 - - + -
456A ASP* 4.1 19.1 - - + +
460A TYR* 3.3 41.8 + - + -
463A VAL* 4.4 23.3 - - + -
466A VAL* 4.8 2.2 - - + -
467A THR* 4.6 7.4 - - + -
472A TYR* 3.9 22.2 - - - +
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Residues in contact with ASP 325 (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 ILE* 3.7 1.7 - - - +
321A ARG* 3.0 47.6 + - - +
322A ILE 3.8 0.4 - - - +
324A LEU* 1.3 75.1 - - - +
326A SER* 1.3 58.6 + - - +
327A TYR 3.4 4.8 - - - +
336A LYS* 4.2 9.2 - - - +
340A LEU* 3.6 24.1 - - + +
344A ARG* 2.8 27.4 + - - +
459A LYS* 4.6 3.2 - - - +
460A TYR* 2.5 28.8 + - - -
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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