Contacts of the helix formed by residues 320 - 328 (chain C) in PDB entry 1KHU
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 ASN 320 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C LEU* 4.3 10.4 - - - +
318C ASN 4.6 4.5 - - - +
319C ARG* 1.3 76.3 - - - +
321C SER* 1.3 64.1 + - - +
322C THR* 3.4 18.2 - - + +
323C ILE* 2.8 39.7 - - - +
324C GLU* 3.0 19.1 + - - +
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Residues in contact with SER 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C ASN* 1.3 71.2 - - - +
322C THR* 1.3 63.4 + - - +
324C GLU* 2.8 12.4 + - - +
325C ASN* 2.7 34.8 + - - +
328C ARG* 5.4 0.2 + - - -
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Residues in contact with THR 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C ASN* 3.4 26.0 + - + +
321C SER* 1.3 81.1 + - - +
323C ILE* 1.3 60.9 + - - +
325C ASN* 3.2 10.1 + - - +
326C THR* 3.0 25.8 + - - -
418C LYS* 5.8 2.4 - - - -
426C ARG* 4.9 8.3 + - - -
433C PRO* 4.7 8.7 - - - +
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Residues in contact with ILE 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C GLU* 3.5 42.6 - - + +
279C LEU* 3.8 29.8 - - + -
316C ASN* 5.1 0.7 - - - +
318C ASN 4.7 4.0 - - - +
319C ARG* 3.7 13.7 - - + -
320C ASN* 2.8 40.9 - - - +
322C THR* 1.3 70.1 - - - +
324C GLU* 1.3 68.2 + - - +
326C THR* 2.9 5.4 + - - -
327C ARG* 2.9 27.0 + - + +
433C PRO* 3.4 32.3 - - + +
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Residues in contact with GLU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A TYR* 3.8 24.3 + - - -
405A GLU* 6.0 0.9 - - - -
408A LYS* 5.6 6.4 - - - -
319C ARG* 3.6 22.5 + - - +
320C ASN 3.0 12.2 + - - +
321C SER* 2.8 14.7 + - - +
323C ILE* 1.3 77.2 - - - +
325C ASN* 1.3 60.5 + - - +
327C ARG* 3.4 16.0 + - - +
328C ARG* 3.2 57.3 + - - +
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Residues in contact with ASN 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A ASN* 3.4 25.5 - - - +
461A ILE* 3.3 27.9 - - - +
321C SER 2.7 15.6 + - - +
322C THR* 3.3 14.8 - - - +
323C ILE 3.1 0.2 - - - -
324C GLU* 1.3 77.3 - - - +
326C THR* 1.3 61.6 + - - +
328C ARG* 3.3 22.2 + - - +
329C HIS* 3.2 16.8 + - - -
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Residues in contact with THR 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ILE* 5.9 2.1 - - - +
322C THR* 3.0 12.2 + - - -
323C ILE 2.9 8.1 + - - -
325C ASN* 1.3 76.2 - - - +
327C ARG* 1.3 63.4 + - - +
329C HIS* 3.0 17.6 + - - +
330C ILE* 3.5 10.0 + - - +
416C PHE* 3.7 11.4 - - + +
417C VAL* 3.6 32.4 - - + +
418C LYS* 4.0 13.7 - - + -
433C PRO* 3.2 27.3 - - + +
434C CYS* 4.1 12.1 - - + -
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Residues in contact with ARG 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A TYR* 3.7 18.8 + - - +
276C TYR* 3.4 26.2 + - - +
278C GLU* 3.0 18.1 + - - -
298C GLY* 5.0 6.8 - - - +
311C LEU* 2.9 25.7 + - - +
312C GLY* 2.6 34.5 + - - -
314C LEU 3.4 9.7 + - - -
319C ARG* 3.3 32.9 - - - +
323C ILE* 2.9 20.1 + - - +
324C GLU* 3.8 14.8 + - - +
325C ASN 3.3 0.2 - - - -
326C THR* 1.3 77.3 - - - +
328C ARG* 1.3 61.8 + - - +
329C HIS 3.2 0.7 + - - -
330C ILE* 3.3 27.0 + - + +
331C GLY 4.6 1.2 + - - -
434C CYS* 3.6 8.7 - - - -
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Residues in contact with ARG 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A PHE* 4.4 22.3 - - + -
401A GLU* 5.0 23.4 + - - +
404A TYR* 3.3 37.6 - - + +
405A GLU* 4.5 16.2 + - - +
408A LYS* 6.0 0.4 - - - +
456A SER* 6.0 2.3 - - - -
459A ASN* 6.0 0.4 - - - +
321C SER 5.4 0.2 + - - -
324C GLU* 3.2 51.3 + - - +
325C ASN* 3.6 20.7 - - - +
326C THR 3.1 1.0 - - - -
327C ARG* 1.3 78.2 - - - +
329C HIS* 1.3 65.6 + - + +
330C ILE 3.5 0.2 - - - -
331C GLY* 4.6 4.6 + - - -
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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