Contacts of the helix formed by residues 374 - 383 (chain J) in PDB entry 3KDO
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 374 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320J ALA* 3.7 29.1 + - + +
369J GLY 2.6 30.5 + - - -
370J LEU* 3.2 11.4 - - - +
371J HIS* 2.3 58.4 + - + +
373J GLY* 1.3 79.6 - - - +
375J ILE* 1.3 60.8 + - - +
376J GLN* 3.3 6.8 + - - +
377J PRO* 3.9 10.1 - - + +
378J VAL* 3.7 15.9 - - - +
440J HIS 5.0 3.1 - - - +
441J VAL 4.3 6.5 - - - +
442J THR* 6.2 0.2 - - - -
443J PRO* 4.4 2.2 - - - +
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Residues in contact with ILE 375 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370J LEU* 4.4 8.3 - - + -
371J HIS 3.2 20.4 - - - +
372J PRO* 4.2 14.6 + - + +
374J ASN* 1.3 82.3 - - - +
376J GLN* 1.3 61.5 + - - +
378J VAL* 4.0 8.5 - - - -
379J ILE* 2.9 34.5 + - + +
388J LEU* 4.5 18.6 - - + -
390J LEU* 4.1 19.5 - - + -
408J VAL* 4.8 7.0 - - + +
411J ALA* 3.9 21.1 - - + -
412J ILE* 4.2 18.4 - - + -
415J ILE* 3.5 20.9 - - + -
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Residues in contact with GLN 376 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373J GLY 6.2 1.1 - - - -
374J ASN* 5.6 0.9 - - - +
375J ILE* 1.3 79.2 - - - +
377J PRO* 1.3 76.7 - - + +
378J VAL 3.3 0.2 + - - -
379J ILE* 3.8 1.7 - - - +
380J GLU* 2.9 23.8 + - - +
415J ILE* 3.8 20.5 - - + +
440J HIS* 5.9 5.8 - - + +
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Residues in contact with PRO 377 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318J ALA* 6.0 1.8 - - - +
320J ALA* 4.9 12.1 - - + -
327J ARG* 5.2 2.2 + - - +
374J ASN* 3.9 15.5 - - - +
375J ILE 3.9 0.7 - - - -
376J GLN* 1.3 98.5 - - + +
378J VAL* 1.3 62.7 + - - +
380J GLU* 3.0 9.1 + - + +
381J ALA* 2.9 27.0 + - - +
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Residues in contact with VAL 378 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317J THR* 3.8 25.1 - - - +
318J ALA* 5.2 4.7 - - - -
320J ALA* 4.3 7.0 - - + -
366J SER* 3.4 29.2 - - - +
370J LEU* 4.9 6.7 - - + -
374J ASN 3.7 18.6 - - - +
375J ILE* 3.9 10.1 - - - +
377J PRO* 1.3 76.8 - - - +
379J ILE* 1.3 64.5 + - + +
380J GLU 3.0 0.5 + - - -
381J ALA* 5.2 0.2 - - - -
382J LEU* 3.0 46.3 + - + +
386J ILE* 4.0 11.4 - - + -
388J LEU* 4.4 6.3 - - + -
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Residues in contact with ILE 379 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J PRO* 4.5 11.7 - - + -
375J ILE* 2.9 24.3 + - + +
376J GLN 4.0 2.2 - - - +
378J VAL* 1.3 76.3 - - + +
380J GLU* 1.3 58.9 + - - +
383J GLY* 3.1 38.3 + - - +
384J THR* 4.2 20.1 - - + +
386J ILE* 4.7 7.2 - - + -
388J LEU* 4.1 26.9 - - + -
412J ILE* 5.1 6.1 - - + -
415J ILE* 3.6 39.9 - - + -
416J MET* 5.9 2.0 - - + -
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Residues in contact with GLU 380 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327J ARG* 4.5 5.9 + - - +
376J GLN 2.9 14.7 + - - +
377J PRO* 3.1 15.5 - - + +
378J VAL 3.0 0.2 - - - -
379J ILE* 1.3 80.8 - - - +
381J ALA* 1.3 61.9 + - + +
382J LEU 3.6 0.3 + - - -
383J GLY* 4.2 2.6 + - - -
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Residues in contact with ALA 381 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318J ALA* 5.0 4.3 - - + -
327J ARG* 3.1 52.7 - - + +
331J LEU* 2.8 31.7 - - + +
377J PRO 2.9 13.0 + - - +
378J VAL 4.2 1.8 - - - +
380J GLU* 1.3 76.1 - - - +
382J LEU* 1.3 66.5 + - + +
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Residues in contact with LEU 382 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315J VAL* 5.0 2.0 - - + -
316J GLY 4.6 1.1 - - - +
318J ALA* 4.6 7.6 - - + -
330J THR* 3.8 24.9 - - + -
331J LEU* 3.8 22.0 - - + +
334J VAL* 3.5 27.4 - - + -
338J ARG* 2.9 36.0 + - - +
366J SER* 4.5 12.8 - - - +
378J VAL* 3.0 35.6 + - + +
381J ALA* 1.3 90.7 - - + +
383J GLY* 1.3 59.8 + - - +
386J ILE* 3.9 17.4 - - + +
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Residues in contact with GLY 383 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338J ARG* 4.6 2.9 - - - -
379J ILE* 3.1 32.2 + - - +
380J GLU 4.2 2.7 + - - -
381J ALA 3.8 0.8 - - - -
382J LEU* 1.3 81.2 - - - +
384J THR* 1.3 64.7 + - - -
385J ASP 3.5 1.5 + - - -
386J ILE* 3.9 11.7 - - - +
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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