Contacts of the helix formed by residues 567 - 577 (chain A) in PDB entry 4KXY
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 GLY 567 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A LEU* 4.1 8.5 - - - -
438A ARG* 4.1 4.6 + - - -
537A ILE* 4.9 0.2 - - - -
560A GLU* 3.5 12.1 - - - -
562A HIS* 3.8 14.3 + - - -
563A TYR 4.8 0.2 - - - -
564A TYR 4.2 4.0 + - - -
565A GLU 3.3 5.7 + - - -
566A GLY* 1.3 79.2 - - - +
568A ILE* 1.3 66.1 + - - -
569A GLY 3.4 2.0 - - - -
570A GLU* 4.0 2.1 - - - +
571A ALA* 3.0 24.2 + - - +
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Residues in contact with ILE 568 (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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434A LEU* 3.8 13.0 - - + -
447A TYR* 4.1 10.3 - - + -
506A ILE* 4.3 11.7 - - + -
507A GLY 5.2 1.3 - - - -
508A ALA* 3.7 32.1 - - + +
534A PRO* 4.7 3.8 - - + -
537A ILE* 3.8 27.8 - - + -
540A LEU* 5.4 2.2 - - + -
558A THR* 3.6 17.9 - - + -
559A VAL 5.0 1.8 - - - +
560A GLU* 2.8 35.8 + - + +
567A GLY* 1.3 73.1 - - - -
569A GLY* 1.3 56.5 + - - +
571A ALA* 3.2 5.7 + - - +
572A VAL* 2.8 43.3 + - + +
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Residues in contact with GLY 569 (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 THR* 3.6 19.4 - - - +
560A GLU* 2.9 10.5 + - - -
568A ILE* 1.3 76.8 - - - +
570A GLU* 1.3 57.0 + - - +
572A VAL* 3.4 1.6 + - - +
573A SER* 2.9 34.0 + - - -
584A VAL* 4.9 1.3 - - - +
586A HIS* 3.5 28.0 - - - -
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Residues in contact with GLU 570 (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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564A TYR* 3.3 19.9 + - - +
565A GLU* 3.8 2.1 - - - +
566A GLY* 2.9 29.1 + - - +
567A GLY 3.5 4.7 + - - +
568A ILE 3.3 0.4 - - - -
569A GLY* 1.3 73.3 - - - +
571A ALA* 1.3 60.5 + - - +
573A SER* 3.8 0.7 - - - -
574A SER* 2.9 35.6 + - - -
586A HIS* 4.0 4.9 - - + +
438B ARG* 2.8 37.8 + - - -
570B GLU* 4.2 19.3 - - + +
571B ALA* 4.4 0.2 - - - -
574B SER* 3.0 32.7 + - - +
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Residues in contact with ALA 571 (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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438A ARG* 3.7 31.3 - - - +
537A ILE* 4.6 11.0 - - + +
540A LEU* 3.7 16.5 - - + +
567A GLY 3.0 19.1 + - - +
568A ILE* 3.4 7.4 - - - +
570A GLU* 1.3 77.4 - - - +
572A VAL* 1.3 57.7 + - - +
574A SER* 3.4 1.9 + - - -
575A ALA* 3.0 28.8 + - - +
570B GLU* 4.6 1.3 - - - -
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Residues in contact with VAL 572 (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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506A ILE* 4.1 23.1 - - + -
540A LEU* 3.9 20.4 - - + -
545A ILE* 4.3 16.6 - - + -
556A ILE* 4.2 15.7 - - + -
558A THR* 4.0 23.3 - - - +
568A ILE* 2.8 33.7 + - + +
569A GLY 3.8 3.4 - - - +
571A ALA* 1.3 70.2 - - - +
573A SER* 1.3 66.0 + - - +
575A ALA* 3.0 12.6 + - - +
576A VAL* 3.1 15.8 + - + +
584A VAL* 4.6 7.0 - - + -
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Residues in contact with SER 573 (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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569A GLY 2.9 18.7 + - - -
570A GLU* 3.9 4.0 - - - -
572A VAL* 1.3 77.0 - - - +
574A SER* 1.3 56.8 + - - +
576A VAL* 4.4 6.5 - - - -
577A VAL* 3.0 34.8 + - - +
584A VAL* 3.6 17.8 - - - +
586A HIS* 5.6 2.8 + - - +
573B SER* 4.2 1.8 - - - -
574B SER* 3.9 28.4 + - - -
577B VAL* 3.7 17.6 - - - +
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Residues in contact with SER 574 (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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570A GLU 2.9 21.9 + - - -
571A ALA 4.0 2.5 - - - -
573A SER* 1.3 76.6 - - - +
575A ALA* 1.3 63.1 + - - +
576A VAL 3.5 0.3 + - - -
577A VAL* 3.8 12.0 - - - +
569B GLY 5.8 0.4 - - - -
570B GLU* 3.0 47.1 + - - +
573B SER* 3.8 15.6 + - - -
586B HIS* 5.9 2.9 - - - -
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Residues in contact with ALA 575 (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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540A LEU* 4.1 16.8 - - + -
542A ARG* 2.7 51.9 + - + +
545A ILE* 5.9 0.9 - - + -
571A ALA 3.0 17.1 + - - +
572A VAL* 3.0 5.8 + - - +
574A SER* 1.3 79.5 - - - +
576A VAL* 1.3 61.4 + - + +
577A VAL 3.7 0.9 - - - +
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Residues in contact with VAL 576 (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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542A ARG* 5.0 1.8 - - + -
545A ILE* 4.2 20.0 - - + -
546A LEU* 3.6 34.3 - - + -
556A ILE* 4.5 3.6 - - + -
572A VAL* 3.1 20.2 + - + +
573A SER 4.1 2.2 - - - +
575A ALA* 1.3 83.4 - - + +
577A VAL* 1.3 70.3 + - - +
579A GLU* 3.0 27.7 + - - +
582A ILE* 3.9 14.0 - - + +
584A VAL* 3.8 28.3 - - + -
577B VAL* 4.3 3.3 - - + +
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Residues in contact with VAL 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ARG* 5.5 1.2 + - - -
573A SER 3.0 20.2 + - - +
574A SER 3.8 12.3 - - - +
575A ALA 5.1 1.2 - - - +
576A VAL* 1.3 77.7 - - - +
578A GLY* 1.3 64.1 + - - +
579A GLU* 3.5 2.1 + - - +
573B SER* 3.8 20.4 - - - +
576B VAL* 4.2 7.6 - - + -
577B VAL* 4.0 30.7 - - + -
578B GLY 5.3 0.2 - - - +
582B ILE 5.0 3.6 - - - +
584B VAL* 4.0 43.7 + - + +
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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