Contacts of the helix formed by residues 557 - 565 (chain A) in PDB entry 4UQG
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 557 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A SER* 3.2 16.3 + - - -
556A THR* 1.3 83.3 - - - +
558A ALA* 1.3 65.6 + - - +
559A ASP* 2.3 28.5 + - - -
560A VAL* 3.0 8.9 + - - +
561A LEU* 3.0 17.0 + - - +
25B T 3.5 20.9 + - - -
26B C 3.5 11.0 - - - -
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Residues in contact with ALA 558 (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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556A THR 3.7 0.8 + - - -
557A SER* 1.3 73.3 - - - +
559A ASP* 1.3 57.4 + - - +
561A LEU* 3.8 1.6 - - - +
562A GLU* 2.9 43.6 + - - +
575A LEU* 4.1 22.2 - - + +
26B C 2.8 31.7 + - + +
27B C 6.1 0.7 - - - +
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Residues in contact with ASP 559 (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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557A SER* 2.3 34.5 + - - -
558A ALA* 1.3 74.6 + - - +
560A VAL* 1.3 65.2 + - - +
562A GLU* 3.8 12.7 + - - +
563A LYS* 3.6 33.5 + - - +
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Residues in contact with VAL 560 (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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539A PHE* 4.8 4.3 - - + -
547A LEU* 4.4 20.6 - - + +
548A LYS* 4.1 21.3 - - + +
555A SER* 3.6 31.4 - - - +
556A THR* 4.7 1.3 - - - -
557A SER* 3.0 23.4 + - - +
559A ASP* 1.3 77.9 - - - +
561A LEU* 1.3 68.6 + - + +
563A LYS* 3.0 17.6 + - - +
564A LEU* 3.2 30.9 + - + +
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Residues in contact with LEU 561 (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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538A LEU* 4.0 25.4 - - + -
539A PHE* 5.1 0.4 - - + -
556A THR* 3.5 27.4 - - + +
557A SER 3.0 15.8 + - - +
558A ALA 3.3 1.3 + - - +
560A VAL* 1.3 77.9 - - + +
562A GLU* 1.3 63.6 + - - +
564A LEU* 2.9 24.5 + - + +
565A ALA* 3.1 2.1 + - - +
571A VAL* 3.1 34.3 - - + +
574A ILE* 3.8 30.1 - - + -
575A LEU* 3.8 28.0 - - + +
578A ARG* 4.2 7.6 - - - +
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Residues in contact with GLU 562 (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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558A ALA* 2.9 34.1 + - - +
559A ASP* 3.9 13.2 - - - +
561A LEU* 1.3 77.4 - - - +
563A LYS* 1.3 62.8 + - + +
564A LEU 3.4 0.3 + - - -
565A ALA* 3.5 14.6 + - - +
566A PRO* 4.1 3.5 - - - +
575A LEU* 4.4 19.3 - - + +
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Residues in contact with LYS 563 (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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547A LEU* 3.7 23.9 - - + +
559A ASP* 3.6 20.9 + - - +
560A VAL* 3.0 10.3 + - - +
562A GLU* 1.3 78.2 - - + +
564A LEU* 1.3 59.6 + - - +
566A PRO* 3.4 14.1 - - - +
567A TYR* 4.2 9.5 - - - -
723A GLN 5.9 0.2 + - - -
726A ASN* 3.2 39.5 + - - +
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Residues in contact with LEU 564 (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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538A LEU* 5.3 0.2 - - + -
539A PHE* 3.5 33.7 - - + -
544A LEU* 4.3 14.4 - - + -
545A PRO* 3.5 37.2 - - + +
547A LEU* 3.7 20.6 - - + -
560A VAL* 3.4 21.1 - - + +
561A LEU* 2.9 18.8 + - + +
563A LYS* 1.3 75.0 - - - +
565A ALA* 1.3 64.9 + - - +
566A PRO* 3.2 4.9 - - - -
567A TYR* 2.9 27.1 + - + +
568A HIS 3.8 2.8 + - - -
571A VAL* 3.9 14.5 - - + +
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Residues in contact with ALA 565 (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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561A LEU 3.1 9.1 + - - +
562A GLU* 3.7 13.2 - - - +
563A LYS 3.5 0.2 - - - -
564A LEU* 1.3 76.0 - - - +
566A PRO* 1.3 68.5 - - + +
567A TYR 3.1 1.4 + - - -
568A HIS 3.2 17.7 + - - +
569A GLU* 5.1 0.3 - - - -
571A VAL* 3.8 18.8 - - + -
572A GLU* 4.8 11.2 - - + +
575A LEU* 5.1 4.5 - - + -
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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