Contacts of the helix formed by residues 513 - 522 (chain A) in PDB entry 6C90
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 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510A ARG* 3.6 4.9 - - - +
511A TRP 3.5 2.9 + - - -
512A ILE* 1.3 77.4 - - - +
514A SER* 1.3 64.9 + - - +
516A GLU* 2.7 33.9 + - - +
517A TYR* 3.0 21.7 + - - +
551A LEU* 4.1 0.7 - - - -
557A ASP* 3.0 30.6 + - - -
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Residues in contact with SER 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A ILE 3.9 0.8 + - - -
513A SER* 1.3 73.9 - - - +
515A GLY* 1.3 56.6 + - - +
517A TYR* 3.7 1.5 - - - +
518A ILE* 2.8 37.1 + - - +
550A GLN 3.5 24.2 - - - -
551A LEU* 3.9 16.5 - - - +
554A GLY* 3.7 13.1 - - - -
555A SER 2.6 26.5 + - - -
557A ASP* 3.9 5.2 + - - -
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Residues in contact with GLY 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A SER* 3.1 3.8 + - - -
514A SER* 1.3 80.0 + - - +
516A GLU* 1.3 59.2 + - - +
518A ILE* 3.4 4.0 + - - +
519A GLN* 2.9 29.7 + - - +
555A SER 4.3 0.2 + - - -
556A ALA* 4.1 8.1 - - - -
557A ASP* 3.5 31.4 + - - -
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Residues in contact with GLU 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A GLU* 3.7 11.0 - - - +
503A LYS* 2.6 39.4 + - - +
510A ARG* 2.8 25.6 + - - -
512A ILE* 3.4 6.0 - - + -
513A SER* 2.7 39.4 + - - +
515A GLY* 1.3 71.6 - - - +
517A TYR* 1.3 65.4 + - - +
519A GLN* 3.3 5.9 + - - +
520A MET* 2.9 46.0 + - + +
557A ASP* 4.3 1.8 + - - +
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Residues in contact with TYR 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A HIS* 3.0 45.1 + + - +
319A TYR 5.3 0.5 + - - -
498A PHE* 3.6 36.1 - + - -
512A ILE* 4.0 17.6 - - + +
513A SER 3.0 15.9 + - - +
514A SER 3.7 3.8 - - - +
516A GLU* 1.3 75.8 - - - +
518A ILE* 1.3 57.0 + - + +
520A MET* 4.4 0.2 - - - +
521A SER* 2.7 47.0 + - - -
535A VAL* 3.2 16.2 - - + +
537A LEU* 4.5 21.4 - - + +
551A LEU* 3.7 30.5 - - + +
552A LEU* 4.1 24.5 - - + +
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Residues in contact with ILE 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A HIS* 4.0 30.2 + - + +
285A THR* 4.6 7.4 - - - +
312A ARG* 4.7 7.0 + - - +
514A SER* 2.8 29.7 + - - +
515A GLY* 3.8 4.9 - - - +
517A TYR* 1.3 75.7 - - + +
519A GLN* 1.3 65.2 + - - +
521A SER* 3.6 6.5 + - - +
522A GLY* 3.0 21.8 + - - -
551A LEU 5.8 0.4 - - - +
554A GLY 3.6 17.3 - - - +
555A SER* 4.3 0.9 - - - -
556A ALA* 3.5 35.4 - - + +
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Residues in contact with GLN 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A THR* 4.2 19.4 + - - +
253A GLU* 4.7 2.8 + - - -
255A HIS* 3.3 21.6 + - + -
284A ALA* 4.1 9.9 - - - +
483A GLU* 5.8 5.2 - - + +
486A ALA* 3.7 24.3 + - + +
487A MET* 3.4 41.8 - - + +
515A GLY 2.9 17.4 + - - +
516A GLU* 3.3 6.9 + - - +
518A ILE* 1.3 80.4 - - - +
520A MET* 1.3 64.2 + - + +
522A GLY* 3.6 6.1 + - - -
523A ARG* 4.0 12.7 + - - +
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Residues in contact with MET 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A PHE* 3.7 45.1 - - + -
394A PHE* 3.9 27.4 - - + -
483A GLU* 3.9 25.4 - - + -
486A ALA* 4.1 11.9 - - + -
496A VAL* 3.7 3.0 - - - +
498A PHE* 3.4 32.5 - - + -
512A ILE* 4.7 2.2 - - + -
516A GLU* 2.9 43.7 + - + +
517A TYR 4.4 0.2 - - - +
519A GLN* 1.3 75.0 - - + +
521A SER* 1.3 65.4 + - - +
522A GLY 3.0 3.0 + - - -
523A ARG* 3.1 19.8 + - - +
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Residues in contact with SER 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A ARG* 5.4 2.1 + - - -
316A LEU* 3.6 20.4 - - - +
318A HIS* 4.4 2.8 - - - -
496A VAL* 4.3 7.6 - - - -
498A PHE* 3.7 7.9 - - - -
517A TYR* 2.7 43.2 + - - -
518A ILE* 3.6 6.8 + - - -
520A MET* 1.3 73.0 - - - +
522A GLY* 1.3 59.6 + - - +
523A ARG 3.1 1.9 + - - -
524A ALA* 3.3 16.6 + - - +
535A VAL* 3.8 27.4 - - - +
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Residues in contact with GLY 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A THR* 3.7 9.6 - - - +
164A SER* 4.5 3.5 + - - -
312A ARG* 3.8 23.2 + - - -
316A LEU* 4.7 0.2 - - - -
492A PRO* 5.7 0.2 - - - +
518A ILE 3.0 20.0 + - - -
519A GLN 4.0 2.7 - - - -
520A MET 3.0 1.2 - - - -
521A SER* 1.3 76.8 + - - +
523A ARG* 1.3 75.1 + - - +
524A ALA 3.2 9.4 + - - +
525A GLY 5.5 0.3 - - - +
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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