Contacts of the helix formed by residues 302 - 311 (chain H) in PDB entry 1QK1
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 ARG 302 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300H ASP* 2.7 39.1 + - - +
301H SER* 1.3 73.6 - - - +
303H PHE* 1.3 63.3 + - - +
304H PRO* 3.4 0.9 - - - -
305H LYS* 3.0 11.3 + - + +
306H ILE* 3.0 29.4 + - + +
362H LEU* 5.0 2.8 - - - +
367H ASP* 3.3 19.6 + - - -
368H ILE* 3.1 44.3 + - - +
369H ARG* 5.2 0.8 - - - +
370H ILE* 3.8 30.0 - - + +
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Residues in contact with PHE 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294H LEU* 4.2 18.8 - - + -
297H LEU* 3.5 44.6 - - + +
298H SER* 3.7 29.6 - - - +
300H ASP* 3.4 17.1 + - - +
301H SER 3.2 0.2 - - - -
302H ARG* 1.3 75.5 - - - +
304H PRO* 1.3 72.7 - - + +
306H ILE* 3.0 13.4 + - + +
307H LEU* 3.0 50.3 + - + +
314H LYS* 3.8 31.9 - - + -
329H PHE* 4.7 5.8 - + - -
331H ILE* 4.8 5.6 - - + -
355H LEU* 4.8 1.3 - - + -
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Residues in contact with PRO 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300H ASP 4.4 1.3 - - - +
301H SER 3.2 17.0 - - - +
302H ARG 3.5 1.1 - - - -
303H PHE* 1.3 96.4 - - + +
305H LYS* 1.3 56.1 + - - +
307H LEU* 3.8 10.0 - - + +
308H GLU* 3.1 28.9 + - - +
314H LYS* 5.9 6.1 - - - -
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Residues in contact with LYS 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301H SER 5.9 0.2 - - - +
302H ARG* 3.0 13.7 + - + +
304H PRO* 1.3 77.8 - - - +
306H ILE* 1.3 67.6 + - - +
308H GLU* 3.4 26.6 + - - +
309H ASN* 3.0 42.9 + - - +
370H ILE* 4.1 25.8 - - + -
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Residues in contact with ILE 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297H LEU* 4.2 15.5 - - + -
302H ARG* 3.0 25.3 + - + +
303H PHE* 3.0 9.2 + - + +
305H LYS* 1.3 77.5 - - - +
307H LEU* 1.3 62.3 + - + +
309H ASN* 3.4 1.7 + - - +
310H LEU* 3.1 28.8 + - + +
354H TYR* 4.3 4.7 - - + -
355H LEU* 3.8 27.6 - - + -
358H CYS* 4.6 7.9 - - - -
368H ILE* 4.0 27.4 - - + -
369H ARG 4.7 6.5 - - - +
370H ILE* 4.2 10.3 - - + -
371H PRO* 3.9 28.0 - - + +
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Residues in contact with LEU 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H PHE* 3.0 53.7 + - + +
304H PRO* 3.8 7.4 - - + +
306H ILE* 1.3 77.4 - - - +
308H GLU* 1.3 63.7 + - - +
310H LEU* 3.1 4.5 + - - +
311H ARG 3.0 17.2 + - - -
312H LEU* 3.0 39.6 + - + +
313H GLN* 4.9 0.7 - - - +
314H LYS* 4.1 26.2 - - + +
331H ILE* 4.7 7.4 - - + -
355H LEU* 3.9 31.4 - - + -
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Residues in contact with GLU 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304H PRO 3.1 17.3 + - - +
305H LYS* 3.4 34.2 + - - +
306H ILE 3.3 0.2 - - - -
307H LEU* 1.3 79.6 - - - +
309H ASN* 1.3 65.3 + - - +
311H ARG* 3.0 20.1 + - - +
312H LEU 4.8 3.1 - - - -
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Residues in contact with ASN 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H LYS* 3.0 40.8 + - - +
306H ILE 3.9 3.6 - - - +
308H GLU* 1.3 80.8 - - - +
310H LEU* 1.3 60.9 + - - +
311H ARG* 3.2 3.1 + - - +
370H ILE* 3.7 14.8 - - - +
371H PRO* 3.0 32.8 + - + +
372H THR 4.4 1.1 - - - +
373H PRO* 3.4 28.1 - - + +
374H VAL* 3.2 27.0 + - - +
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Residues in contact with LEU 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306H ILE* 3.1 21.5 + - + +
307H LEU* 3.1 6.0 + - - +
309H ASN* 1.3 75.8 - - - +
311H ARG* 1.3 73.8 + - - +
312H LEU* 3.7 15.4 - - + +
347H LEU* 3.6 16.6 - - - +
350H ASP 5.6 0.7 - - - -
351H GLY* 3.7 24.7 - - - +
354H TYR* 4.1 12.6 - - + -
355H LEU* 3.6 31.2 - - + -
371H PRO* 3.9 22.7 - - + -
372H THR 5.2 3.1 - - - +
374H VAL* 4.1 12.1 - - + +
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Residues in contact with ARG 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H ASN* 3.6 28.7 + - - +
307H LEU 3.0 2.4 + - - -
308H GLU* 3.0 14.9 + - - +
309H ASN 4.1 3.6 - - - +
310H LEU* 1.3 81.2 - - - +
312H LEU* 1.3 62.0 + - - +
334H LEU* 3.2 48.3 + - + +
335H ASP* 3.2 40.9 + - - +
339H LYS* 4.1 6.3 - - - +
347H LEU* 4.0 10.3 - - + +
374H VAL* 3.2 40.2 - - + -
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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
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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