Contacts of the helix formed by residues 420 - 427 (chain D) in PDB entry 5COX
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 THR 420 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D GLY* 4.8 2.1 - - - -
419D LEU* 1.3 74.1 + - - +
421D GLN* 1.3 55.8 + - - +
422D PHE 2.7 12.5 + - - -
423D VAL* 2.9 3.6 + - - +
424D GLU* 2.8 35.1 + - - +
572D VAL* 3.7 8.7 - - + +
573D LYS* 3.3 23.6 - - + +
574D GLY* 3.5 21.8 - - - +
576D PRO* 3.2 29.2 - - + -
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Residues in contact with GLN 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D ILE* 3.4 17.0 - - - +
398D GLU* 2.9 52.0 + - + +
417D HIS* 3.5 23.1 + - + +
418D GLY 3.5 6.5 + - - +
420D THR* 1.3 76.3 + - - +
422D PHE* 1.3 58.9 + - - +
424D GLU* 3.2 17.9 + - - +
425D SER* 2.8 20.8 + - - -
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Residues in contact with PHE 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D MET* 4.4 0.2 - - - +
296D PRO* 3.9 25.8 - - + -
300D MET* 4.1 13.5 - - + -
397D ILE* 3.9 20.9 - - + -
413D ILE* 3.8 13.0 - - + -
414D LEU* 3.2 51.6 - - + -
417D HIS* 3.6 20.9 - - + -
418D GLY 2.9 24.7 - - - +
419D LEU* 3.2 10.3 - - - +
420D THR 2.7 1.4 + - - -
421D GLN* 1.3 69.7 - - - +
423D VAL* 1.3 64.6 + - - +
424D GLU 3.4 1.6 - - - +
425D SER* 4.0 8.5 - - - -
426D PHE* 3.2 53.6 + + - +
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Residues in contact with VAL 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D MET* 3.8 14.6 - - - +
300D MET* 4.1 14.1 - - + -
304D ILE* 4.4 3.4 - - + -
419D LEU 2.8 19.4 + - - +
420D THR* 3.6 3.1 - - - +
422D PHE* 1.3 77.3 - - - +
424D GLU* 1.3 61.3 + - - +
426D PHE* 3.3 1.4 + - - +
427D THR* 2.6 33.6 + - - +
568D ILE* 3.8 26.5 - - + -
572D VAL* 4.3 8.7 - - + -
576D PRO* 3.8 24.0 - - + -
577D PHE 4.3 1.1 - - - +
578D THR* 3.5 25.6 - - + -
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Residues in contact with GLU 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D GLU* 4.0 11.1 - - - +
420D THR* 2.8 20.1 + - - +
421D GLN* 3.2 38.6 + - - +
423D VAL* 1.3 78.4 - - - +
425D SER* 1.3 61.2 + - - +
427D THR 3.2 0.9 + - - -
428D ARG* 2.8 51.2 + - - +
576D PRO* 4.4 18.6 - - + +
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Residues in contact with SER 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D ASN 3.6 12.9 - - - +
397D ILE* 3.6 5.8 - - - -
398D GLU* 3.0 39.2 + - - +
421D GLN* 2.8 30.5 + - - -
422D PHE* 3.9 7.6 + - - -
423D VAL 3.4 0.4 - - - -
424D GLU* 1.3 76.0 - - - +
426D PHE* 1.3 58.9 + - - +
428D ARG* 2.7 27.8 - - - +
429D GLN* 3.8 4.9 - - - +
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Residues in contact with PHE 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D ASN* 3.3 1.9 - - - +
196D MET* 3.0 50.8 + - + +
197D MET* 3.6 29.3 + - + +
200D PHE* 3.3 41.5 - + - -
297D GLY* 4.4 2.0 - - - -
300D MET* 4.0 7.0 - - + -
395D PHE* 5.0 4.3 - - + -
396D ASN 4.4 4.9 - - - -
397D ILE* 3.6 37.0 - - + -
407D PHE* 3.8 8.5 - + - -
422D PHE* 3.2 35.0 + + - +
425D SER* 1.3 78.0 - - - +
427D THR* 1.3 66.0 + - - +
428D ARG 3.0 2.8 + - - -
429D GLN* 3.8 10.0 + - - -
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Residues in contact with THR 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D ASN* 2.8 29.4 + - - +
197D MET* 4.8 2.2 - - - +
423D VAL 2.6 19.9 + - - -
424D GLU 3.2 0.2 + - - -
426D PHE* 1.3 76.0 - - - +
428D ARG* 1.3 93.4 + - - +
577D PHE* 3.5 17.5 + - + -
578D THR* 3.1 28.4 - - - +
579D SER 4.2 2.0 - - - +
581D ASN 4.5 2.5 - - - +
582D VAL* 3.3 7.1 - - - -
583D GLN* 3.0 21.8 - - - +
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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