Contacts of the helix formed by residues 503 - 514 (chain D) in PDB entry 7C17
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 SER 503 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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812C PHE* 3.5 21.0 - - - -
813C GLU* 4.5 2.9 - - - -
451D PRO 4.2 4.7 + - - -
452D LEU* 4.4 1.5 + - - +
455D ALA* 3.3 32.7 + - - +
501D VAL* 3.2 8.1 + - - +
502D PRO* 1.3 72.5 - - - +
504D GLN* 1.3 71.3 + - - +
505D ASP 3.5 1.6 - - - -
506D VAL* 3.3 10.1 - - - +
507D VAL* 2.7 33.9 + - - +
598D LYS* 5.9 3.8 - - - -
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Residues in contact with GLN 504 (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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812C PHE* 4.5 1.5 - - - +
813C GLU* 3.3 33.8 + - - +
1101C LEU* 3.4 21.3 - - + +
455D ALA* 6.0 2.4 - - - +
503D SER* 1.3 79.2 - - - +
505D ASP* 1.3 57.7 + - - +
507D VAL* 3.3 10.6 - - - +
508D LEU* 2.9 29.6 + - - +
598D LYS* 6.2 0.9 - - + -
730D ALA* 3.3 22.3 - - - +
731D ARG* 3.1 44.6 - - + +
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Residues in contact with ASP 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806C PRO* 3.4 28.2 - - - +
809C GLY* 3.4 26.4 + - - -
811C ASN* 3.6 15.0 - - - +
812C PHE* 3.5 35.0 + - + +
1100C PRO* 5.3 0.2 - - - +
1101C LEU* 3.4 21.8 - - + +
503D SER 3.5 0.2 - - - -
504D GLN* 1.3 78.7 + - - +
506D VAL* 1.3 60.4 + - - +
508D LEU* 3.2 4.0 + - - +
509D GLY* 3.0 23.2 + - - -
629D PHE* 5.4 0.9 - - - -
632D ALA* 4.4 8.3 - - - +
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Residues in contact with VAL 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812C PHE* 3.7 22.5 - - + -
452D LEU* 4.4 6.5 - - + -
502D PRO* 3.7 15.3 - - + -
503D SER 3.3 28.5 - - - +
505D ASP* 1.3 78.9 - - - +
507D VAL* 1.3 60.0 + - - +
509D GLY* 3.3 1.0 + - - +
510D LEU* 2.9 33.5 + - + +
624D ILE 3.8 4.5 - - - +
625D MET* 3.8 27.6 - - + +
628D GLY* 3.7 28.2 - - - -
629D PHE* 5.1 0.9 - - - +
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Residues in contact with VAL 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D PRO* 3.8 13.5 - - - +
503D SER 2.7 27.5 + - - +
504D GLN* 3.3 15.0 - - - +
506D VAL* 1.3 71.0 - - - +
508D LEU* 1.3 61.7 + - - +
510D LEU* 4.4 4.0 - - - -
511D TYR* 2.9 28.9 + - + +
596D LEU 4.9 2.2 - - - +
597D GLY* 4.5 2.0 - - - +
598D LYS* 4.2 28.5 - - + +
601D ILE* 3.7 26.5 - - + -
728D SER* 5.2 3.7 + - - +
730D ALA* 3.8 22.4 - - + +
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Residues in contact with LEU 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806C PRO* 5.0 5.2 - - + -
1100C PRO* 5.3 0.4 - - + -
1101C LEU* 3.7 24.0 - - + -
504D GLN 2.9 19.0 + - - +
505D ASP* 3.2 5.6 + - - +
507D VAL* 1.3 76.3 - - - +
509D GLY* 1.3 59.5 + - - +
511D TYR* 3.4 3.6 + - + +
512D TYR* 2.9 28.6 + - - +
637D ALA* 3.8 22.4 - - + +
724D MET* 3.8 37.2 - - + +
725D MET* 3.7 41.5 - - + -
730D ALA* 4.1 7.6 - - + -
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Residues in contact with GLY 509 (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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505D ASP 3.0 11.5 + - - -
506D VAL 3.3 3.3 + - - -
508D LEU* 1.3 78.1 - - - +
510D LEU* 1.3 58.0 + - - +
512D TYR* 3.4 7.7 + - - +
513D MET* 2.9 26.9 + - - +
628D GLY* 4.1 7.2 - - - -
631D TYR* 4.4 7.2 - - - +
632D ALA* 3.8 29.3 - - - +
635D SER* 5.4 1.1 - - - -
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Residues in contact with LEU 510 (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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502D PRO* 4.9 8.5 - - + -
506D VAL* 2.9 25.4 + - + +
507D VAL 3.9 3.8 - - - +
509D GLY* 1.3 75.0 - - - +
511D TYR* 1.3 60.8 + - - +
513D MET* 3.1 5.4 + - + +
514D THR* 2.9 30.9 + - - +
579D LEU* 3.7 40.6 - - + +
596D LEU* 5.4 2.2 - - + +
601D ILE* 3.8 29.8 - - + -
604D MET* 6.3 2.5 - - - -
624D ILE* 4.1 18.6 - - + +
627D THR 4.6 0.9 - - - +
628D GLY* 3.7 25.4 - - - +
631D TYR* 6.1 0.4 - - + -
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Residues in contact with TYR 511 (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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507D VAL 2.9 19.8 + - - +
508D LEU* 3.8 4.9 - - - +
510D LEU* 1.3 73.0 - - - +
512D TYR* 1.3 64.3 + - - +
514D THR* 3.5 6.2 + - + +
515D ARG* 3.3 53.6 + - + +
595D ALA* 3.2 34.7 - - + +
596D LEU 4.0 7.8 + - - +
597D GLY 5.5 0.2 - - - -
717D VAL* 3.9 12.6 - - - +
723D TYR* 4.5 1.8 + - - -
724D MET* 3.6 50.9 - - + -
727D ASP* 2.9 30.6 + - - +
728D SER* 3.6 25.4 - - - +
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Residues in contact with TYR 512 (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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1222C GLU* 3.3 36.7 + - - +
1223C ARG* 3.3 36.0 - - - +
508D LEU 2.9 17.0 + - - +
509D GLY 3.7 5.4 - - - +
510D LEU 3.3 0.2 - - - -
511D TYR* 1.3 77.6 - - - +
513D MET* 1.3 58.5 + - - +
515D ARG* 4.6 3.1 - - + -
537D TYR* 5.2 0.2 - - - -
544D LEU* 3.5 22.7 - - + +
545D HIS* 3.2 46.3 + + - -
631D TYR 4.4 2.0 - - - -
634D ARG 4.8 0.2 - - - -
635D SER* 3.6 41.1 - - - -
637D ALA* 5.6 1.3 - - + -
719D PHE* 4.8 1.8 - + - -
724D MET* 3.7 26.7 - - + -
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Residues in contact with MET 513 (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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509D GLY 2.9 14.3 + - - +
510D LEU* 3.1 11.6 + - + +
512D TYR* 1.3 79.2 - - - +
514D THR* 1.3 55.7 + - - +
515D ARG 3.3 4.5 + - - +
544D LEU* 3.8 25.8 - - + +
573D THR* 4.3 0.7 - - - +
575D GLY* 3.3 26.4 + - - +
576D ARG 4.1 0.2 + - - -
579D LEU* 3.7 28.3 - - + -
631D TYR* 5.0 10.3 - - + -
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Residues in contact with THR 514 (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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510D LEU 2.9 19.8 + - - +
511D TYR* 3.6 12.3 - - + +
513D MET* 1.3 74.9 - - - +
515D ARG* 1.3 61.2 + - - +
573D THR* 4.4 2.0 - - - -
576D ARG* 2.6 58.8 + - - +
579D LEU* 6.3 2.7 - - - -
594D GLN 3.4 7.1 + - - -
595D ALA* 3.3 25.5 - - - +
596D LEU* 3.7 18.8 - - + +
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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