Contacts of the helix formed by residues 513 - 522 (chain B) in PDB entry 6IEH
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510B ARG* 4.5 5.4 - - - -
511B TRP 3.5 2.2 + - - -
512B ILE* 1.3 76.5 - - - +
514B SER* 1.3 64.9 + - - +
515B GLY* 3.2 6.5 + - - -
516B GLU* 2.9 36.6 + - - +
517B TYR* 2.9 21.0 + - - +
551B LEU* 5.1 1.3 - - - -
557B ASP* 4.2 10.7 + - - -
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Residues in contact with SER 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B SER* 1.3 72.2 - - - +
515B GLY* 1.3 56.4 + - - +
517B TYR* 3.3 0.3 + - - +
518B ILE* 2.8 34.9 + - - +
550B GLN* 2.5 47.2 + - - +
551B LEU* 4.0 12.4 - - - +
554B GLY* 3.4 8.5 - - - -
555B SER 2.9 27.1 - - - -
557B ASP* 6.0 0.2 - - - -
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Residues in contact with GLY 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B SER* 3.2 6.0 + - - -
514B SER* 1.3 78.7 - - - +
516B GLU* 1.3 61.0 + - - +
518B ILE* 3.7 7.3 - - - +
519B GLN* 3.1 24.8 + - - +
555B SER 4.0 1.8 + - - -
556B ALA* 4.2 13.9 - - - +
557B ASP* 3.9 21.3 + - - -
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Residues in contact with GLU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B GLU* 4.2 14.8 - - - +
503B LYS* 3.2 23.1 + - - -
510B ARG* 2.7 38.6 + - - -
512B ILE* 3.3 12.7 - - + +
513B SER* 2.9 30.5 + - - +
515B GLY* 1.3 75.4 - - - +
517B TYR* 1.3 64.3 + - - +
519B GLN* 3.7 3.0 + - - +
520B MET* 3.5 32.9 + - + +
557B ASP* 4.9 0.4 + - - +
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Residues in contact with TYR 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B HIS* 3.1 37.7 - + - +
319B TYR 5.5 1.2 + - - -
331B VAL* 5.9 0.2 - - - +
498B PHE* 3.7 35.4 - + - -
512B ILE* 4.0 12.0 - - + +
513B SER 2.9 13.1 + - - +
514B SER 3.7 5.8 - - - +
516B GLU* 1.3 73.2 - - - +
518B ILE* 1.3 75.3 + - + +
519B GLN 3.3 0.2 + - - -
520B MET 3.4 0.7 + - - -
521B SER* 3.0 42.5 + - - -
535B VAL* 3.8 7.3 - - + +
537B LEU* 4.3 17.2 - - + +
551B LEU* 3.5 34.3 - - + +
552B LEU* 3.9 26.4 - - + +
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Residues in contact with ILE 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B HIS* 4.9 21.5 - - + +
285B THR* 5.0 2.9 - - - +
312B ARG* 5.5 2.6 + - - +
514B SER 2.8 23.7 + - - +
515B GLY* 3.7 8.3 - - - +
517B TYR* 1.3 94.2 - - + +
519B GLN* 1.3 64.0 + - - +
521B SER* 3.9 4.6 + - - +
522B GLY* 3.4 17.5 + - - -
551B LEU 4.7 1.8 - - - +
552B LEU 4.5 8.3 - - - +
554B GLY 4.1 19.3 - - - +
556B ALA* 4.8 19.1 - - + +
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Residues in contact with GLN 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B THR* 4.8 11.5 + - - +
253B GLU* 4.9 4.0 + - - -
255B HIS* 4.4 23.4 + - - -
256B TYR* 4.6 5.5 + - - -
258B ARG* 5.8 0.5 + - - -
486B ALA* 3.8 30.9 + - + +
487B MET* 4.1 27.6 - - + +
515B GLY 3.1 14.5 + - - +
516B GLU* 4.2 4.5 - - - +
517B TYR 3.3 0.2 - - - -
518B ILE* 1.3 81.9 - - - +
520B MET* 1.3 61.6 + - + +
522B GLY* 3.5 10.2 + - - -
523B ARG* 3.8 13.0 - - - +
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Residues in contact with MET 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B PHE* 3.7 35.5 - - + -
394B PHE* 3.9 17.3 - - + -
483B GLU* 3.4 37.2 - - + +
486B ALA* 4.2 14.8 - - + -
496B VAL* 3.6 12.0 - - - +
498B PHE* 3.3 33.2 - - + -
512B ILE* 5.5 1.3 - - + -
516B GLU* 3.5 23.3 + - + +
517B TYR 3.4 1.8 + - - -
519B GLN* 1.3 78.2 - - + +
521B SER* 1.3 56.8 + - - +
522B GLY 3.2 0.9 - - - -
523B ARG* 3.2 26.8 - - - +
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Residues in contact with SER 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG* 5.5 1.4 + - - -
316B LEU* 3.7 16.6 - - - +
318B HIS* 4.4 5.9 + - - -
496B VAL* 4.5 2.0 - - - -
498B PHE* 4.2 3.1 - - - -
517B TYR* 3.0 39.4 + - - -
518B ILE* 3.9 6.6 + - - +
520B MET* 1.3 73.6 - - - +
522B GLY* 1.3 55.6 + - - +
523B ARG 3.2 7.1 + - - -
524B ALA* 3.6 18.2 + - - +
535B VAL* 3.7 32.0 - - - +
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Residues in contact with GLY 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B THR* 4.4 23.3 - - - +
164B SER* 4.9 3.3 + - - -
312B ARG* 3.7 27.9 + - - -
518B ILE 3.4 14.7 + - - -
519B GLN 3.9 4.7 - - - -
520B MET 3.2 1.2 - - - -
521B SER* 1.3 76.1 + - - +
523B ARG* 1.3 64.0 + - - +
524B ALA 3.2 2.9 - - - +
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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