Contacts of the helix formed by residues 513 - 522 (chain B) in PDB entry 1GKU
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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511B VAL* 3.6 2.4 - - - +
512B GLU* 1.3 83.3 + - - +
514B PRO* 1.3 62.3 - - - +
515B THR 4.5 1.1 - - - -
516B LYS* 3.0 21.9 + - - +
517B ALA* 2.7 34.3 + - - +
551B ALA* 3.6 5.4 - - - +
803B GLU* 2.4 32.1 + - - +
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Residues in contact with PRO 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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512B GLU 4.3 0.2 - - - +
513B SER* 1.3 86.6 - - - -
515B THR* 1.3 52.5 + - - +
517B ALA* 3.0 6.5 + - + +
518B ARG* 2.6 68.8 + - - +
538B TYR* 5.6 0.9 - - + -
551B ALA* 3.6 13.0 - - + -
553B ILE* 4.0 23.3 - - + -
612B ARG* 5.8 0.4 - - - +
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Residues in contact with THR 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* 3.3 1.0 - - - -
514B PRO* 1.3 77.8 - - - +
516B LYS* 1.3 54.6 + - - +
518B ARG* 3.6 2.8 + - - +
519B GLN* 2.7 43.6 + - + +
803B GLU* 4.0 22.3 + - + +
804B ASN* 2.9 35.9 - - - +
870B GLU* 3.0 39.1 + - + +
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Residues in contact with LYS 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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511B VAL* 3.8 16.1 - - + +
512B GLU* 3.0 25.7 + - - +
513B SER* 3.0 24.1 + - - +
515B THR* 1.3 79.5 - - - +
517B ALA* 1.3 64.3 + - - +
519B GLN* 3.6 1.3 - - - +
520B ILE* 3.0 31.2 + - + +
629B GLY 2.9 27.9 + - - -
630B THR 3.8 0.2 - - - -
631B ASP* 3.2 22.3 + - - +
658B PHE* 3.9 20.2 - - - -
661B VAL* 4.1 25.4 - - + -
802B PHE* 4.7 4.7 - - + -
803B GLU* 3.9 19.3 - - + +
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Residues in contact with ALA 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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511B VAL* 3.8 19.9 - - + +
513B SER 2.7 16.0 + - - +
514B PRO* 3.3 11.9 - - + +
516B LYS* 1.3 72.9 - - - +
518B ARG* 1.3 61.4 + - - +
520B ILE* 3.6 0.6 + - - -
521B SER* 3.4 19.6 + - - -
538B TYR* 4.3 14.4 - - + -
549B VAL* 3.5 24.8 - - + +
550B THR* 4.2 12.8 - - - -
551B ALA* 4.3 2.5 - - + +
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Residues in contact with ARG 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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514B PRO* 2.6 51.2 + - - +
515B THR* 3.6 5.2 + - - +
517B ALA* 1.3 69.8 - - - +
519B GLN* 1.3 66.8 + - - +
521B SER* 2.9 22.0 + - - -
522B ARG* 3.1 38.7 + - - +
538B TYR* 3.2 38.3 + - + +
870B GLU* 2.7 40.4 + - - +
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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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515B THR* 2.7 33.2 + - + +
516B LYS* 3.6 4.0 - - - +
518B ARG* 1.3 74.6 - - - +
520B ILE* 1.3 64.1 + - - +
522B ARG* 3.4 35.7 + - - +
523B PHE* 3.5 27.0 + - + -
661B VAL* 4.5 7.6 - - + -
803B GLU 3.5 20.4 - - - +
804B ASN* 3.0 33.9 + - - +
868B VAL* 3.0 27.5 + - - +
869B VAL* 4.3 3.9 - - - +
870B GLU* 5.1 1.6 - - - +
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Residues in contact with ILE 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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509B PHE* 3.7 35.7 - - + -
511B VAL* 4.0 14.8 - - + -
516B LYS* 3.0 26.0 + - + +
517B ALA* 4.0 3.8 - - - +
519B GLN* 1.3 76.2 - - - +
521B SER* 1.3 64.5 + - - +
523B PHE* 2.9 32.3 + - + +
524B PHE* 3.9 14.5 - - + -
547B LEU* 5.2 2.5 - - + -
549B VAL* 4.8 11.9 - - + -
658B PHE* 4.1 14.1 - - + -
661B VAL* 4.0 15.3 - - + -
666B ILE* 4.1 20.9 - - + -
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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
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517B ALA 3.4 12.1 + - - -
518B ARG* 2.9 21.9 + - - -
520B ILE* 1.3 79.5 - - - +
522B ARG* 1.3 56.0 + - - +
524B PHE* 3.0 24.4 + - - +
525B GLY 3.6 9.0 + - - +
527B PRO* 3.5 32.3 - - - +
538B TYR* 4.0 15.5 - - - +
540B ILE* 4.0 16.8 - - - +
549B VAL* 4.6 8.9 - - - +
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Residues in contact with ARG 522 (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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518B ARG* 3.1 51.6 + - - +
519B GLN* 3.4 34.4 + - - +
520B ILE 3.1 0.4 - - - -
521B SER* 1.3 74.1 + - - +
523B PHE* 1.3 61.6 + - + +
524B PHE 3.0 6.9 + - - -
525B GLY* 3.4 21.2 + - - +
527B PRO* 4.9 6.1 - - + -
868B VAL* 3.7 33.5 - - - +
870B GLU* 3.7 14.3 + - - +
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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