Contacts of the helix formed by residues 556 - 571 (chain A) in PDB entry 4Z4H
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 THR 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A ARG* 4.6 18.6 - - - +
555A THR* 1.3 82.7 - - - +
557A PRO* 1.3 76.0 - - - +
558A GLN* 3.5 7.3 + - - +
559A THR* 3.2 29.8 + - - +
560A LEU* 3.1 27.9 + - - +
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Residues in contact with PRO 557 (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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477A ILE* 4.6 22.0 - - + +
556A THR* 1.3 89.6 - - - +
558A GLN* 1.3 56.6 + - - +
560A LEU* 4.2 3.0 - - + +
561A SER* 3.0 30.8 + - - -
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Residues in contact with GLN 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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436A ASP* 6.3 1.0 - - - +
556A THR* 3.2 7.5 + - - +
557A PRO* 1.3 76.7 - - - +
559A THR* 1.3 61.5 + - - +
561A SER* 3.5 7.1 + - - -
562A ASN* 3.0 42.6 + - - +
794A THR* 5.7 1.2 + - - -
8D A 2.7 61.7 + - + +
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Residues in contact with THR 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ASN* 4.7 18.6 + - + +
555A THR* 5.7 1.1 - - - -
556A THR* 3.2 25.6 + - - +
558A GLN* 1.3 75.8 - - - +
560A LEU* 1.3 63.1 + - + +
562A ASN* 3.1 4.9 + - - +
563A LEU* 2.8 29.7 + - + +
2B U 3.4 56.6 + - + +
8D A 4.5 5.4 + - - -
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Residues in contact with LEU 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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470A PHE* 3.8 32.1 - - + -
473A GLN* 3.7 27.8 - - + -
474A LEU* 4.2 22.3 - - + +
477A ILE* 4.0 27.8 - - + -
551A ASN 5.5 0.7 - - - +
555A THR* 3.7 19.5 - - - +
556A THR 3.1 19.8 + - - +
557A PRO* 4.2 1.1 - - + +
559A THR* 1.3 81.0 - - + +
561A SER* 1.3 62.4 + - - +
563A LEU* 3.2 10.3 + - + +
564A CYS* 3.0 27.5 + - - -
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Residues in contact with SER 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A MET* 4.5 18.0 - - - +
477A ILE* 3.8 14.5 - - - +
481A THR* 4.4 9.7 + - - -
557A PRO 3.0 21.9 + - - -
558A GLN* 3.6 12.4 + - - -
560A LEU* 1.3 77.1 - - - +
562A ASN* 1.3 62.6 + - - +
564A CYS* 3.1 15.9 + - - +
565A LEU* 3.2 16.0 + - - +
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Residues in contact with ASN 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 GLN* 3.0 31.2 + - - +
559A THR 3.1 3.1 + - - +
561A SER* 1.3 77.5 + - - +
563A LEU* 1.3 61.4 + - - +
565A LEU* 3.2 36.0 + - - +
566A LYS* 3.5 7.8 + - - +
792A ARG 4.7 6.7 - - - +
793A CYS* 4.9 4.2 - - - +
794A THR* 5.3 3.1 + - - +
2B U 2.9 41.9 + - + +
3B C 4.0 14.4 + - - +
8D A 3.8 17.4 + - - -
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Residues in contact with LEU 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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470A PHE* 4.1 21.8 - - + -
474A LEU* 4.4 14.1 - - + -
519A VAL* 6.3 0.4 - - + -
545A GLN* 3.6 34.8 - - + +
547A VAL* 3.9 26.2 - - + -
559A THR* 2.8 17.2 + - + +
560A LEU* 3.3 14.1 - - + +
561A SER 3.1 0.2 - - - -
562A ASN* 1.3 77.9 - - - +
564A CYS* 1.3 60.0 + - - +
566A LYS* 3.4 7.2 + - + +
567A ILE* 3.2 37.4 + - + +
2B U 3.6 25.7 + - - +
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Residues in contact with CYS 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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442A PHE* 3.8 2.8 - - + -
474A LEU* 3.8 22.2 - - - -
477A ILE* 4.1 9.0 - - - -
478A SER* 4.0 17.5 - - - -
481A THR* 3.8 19.5 - - + +
483A MET* 3.6 24.1 - - + +
560A LEU 3.0 16.5 + - - -
561A SER* 3.1 9.4 + - - +
563A LEU* 1.3 75.8 - - - +
565A LEU* 1.3 64.2 + - - +
567A ILE* 4.3 2.7 - - - -
568A ASN* 3.0 27.4 + - - +
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Residues in contact with LEU 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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437A MET* 3.5 19.1 - - + -
442A PHE* 3.4 28.0 - - + -
561A SER* 3.2 16.4 + - - +
562A ASN* 3.2 21.1 + - - +
564A CYS* 1.3 77.8 - - - +
566A LYS* 1.3 61.3 + - - +
569A VAL* 3.2 16.9 + - - +
575A ASN* 3.1 23.8 + - + +
576A ASN* 6.3 0.9 - - - +
791A VAL 3.4 14.1 - - - +
792A ARG 3.7 6.3 - - - +
793A CYS* 3.6 37.2 - - - +
794A THR* 4.3 9.2 - - + +
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Residues in contact with LYS 566 (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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545A GLN* 3.3 20.4 - - - +
562A ASN 3.5 6.9 + - - +
563A LEU* 3.4 8.6 + - + +
564A CYS 3.2 0.4 - - - -
565A LEU* 1.3 77.1 - - - +
567A ILE* 1.3 60.1 + - - +
569A VAL* 3.3 6.4 + - - +
570A LYS* 2.9 34.6 + - - +
791A VAL* 6.2 0.7 - - - -
792A ARG* 3.3 17.1 - - + +
859A ALA* 2.6 40.4 + - - +
1B U 2.9 31.2 + - - -
2B U 3.3 29.4 + - - +
3B C 2.7 27.4 + - - +
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Residues in contact with ILE 567 (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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448A ILE* 3.8 13.0 - - + -
474A LEU* 4.8 17.5 - - + -
483A MET* 3.6 20.2 - - + -
485A ILE* 5.8 2.5 - - + -
517A LEU* 3.8 29.6 - - + -
519A VAL* 5.1 3.6 - - + -
545A GLN* 3.9 29.4 - - + -
563A LEU* 3.2 30.7 + - + +
564A CYS* 3.3 6.7 + - - +
566A LYS* 1.3 75.6 - - - +
568A ASN* 1.3 62.7 + - - +
570A LYS* 3.3 6.5 + - - -
571A LEU* 3.0 28.4 + - + +
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Residues in contact with ASN 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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442A PHE* 3.3 27.6 - - + -
444A THR 3.4 17.8 + - - -
445A GLY* 3.3 2.1 - - - -
446A ILE* 2.8 30.8 + - - +
483A MET* 3.3 14.8 - - - +
564A CYS 3.0 16.6 + - - +
567A ILE* 1.3 76.3 - - - +
569A VAL* 1.3 55.8 + - - +
571A LEU* 3.3 6.6 + - - +
572A GLY 3.2 5.2 + - - -
573A GLY* 2.7 38.3 + - - -
574A VAL 3.5 3.6 - - - +
575A ASN* 3.0 22.1 + - - +
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Residues in contact with VAL 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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565A LEU 3.2 15.2 + - - +
566A LYS* 3.3 7.5 + - - +
567A ILE 3.3 0.2 - - - -
568A ASN* 1.3 76.5 - - - +
570A LYS* 1.3 59.2 + - - +
572A GLY 2.9 9.5 + - - -
573A GLY 4.1 6.5 - - - +
575A ASN* 3.4 21.5 - - - +
623A ASN* 5.7 0.7 - - - +
624A ARG* 2.7 30.7 + - - +
791A VAL* 3.6 27.1 - - + -
856A MET* 3.5 45.6 - - + +
859A ALA* 4.3 8.3 - - + -
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Residues in contact with LYS 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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517A LEU* 5.3 1.8 - - + -
533A LYS* 3.9 3.5 - - - +
543A ALA* 4.8 0.8 - - + +
544A THR 3.0 27.5 + - - +
545A GLN* 2.6 30.9 + - + +
566A LYS* 2.9 18.3 + - - +
567A ILE* 3.3 7.8 + - - +
569A VAL* 1.3 76.0 - - - +
571A LEU* 1.3 68.9 + - + +
572A GLY* 3.2 1.3 + - - -
624A ARG* 5.4 0.5 + - - -
855A THR* 4.8 6.2 - - - +
856A MET 3.7 21.0 + - - +
857A TYR 4.0 11.4 - - - -
859A ALA* 3.2 26.8 + - + -
905A IPH 3.7 34.9 - - + -
1B U 3.4 20.6 + - - -
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Residues in contact with LEU 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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446A ILE* 3.6 29.2 - - + +
448A ILE* 3.6 39.3 - - + -
483A MET* 5.4 0.4 - - - -
516A GLN* 3.8 31.0 - - + +
517A LEU* 3.9 28.0 - - + -
543A ALA* 4.1 4.9 - - + -
567A ILE* 3.0 24.1 + - + +
568A ASN 3.9 3.6 - - - +
569A VAL 3.1 0.4 - - - -
570A LYS* 1.3 84.5 - - + +
572A GLY* 1.3 59.6 + - - +
573A GLY 3.5 1.6 - - - -
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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