Contacts of the helix formed by residues 563 - 575 (chain A) in PDB entry 1GM5
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 ARG 563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A VAL* 4.0 22.6 - - + +
560A PRO* 4.0 30.6 - - + +
561A MET 2.0 8.1 + - - +
562A ASP* 1.3 92.5 + - - +
564A VAL* 1.3 55.6 + - - +
565A ASN* 3.3 2.0 - - - -
566A GLU* 1.8 88.2 + - + +
567A VAL 3.8 1.4 + - - -
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Residues in contact with VAL 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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560A PRO 4.6 2.5 - - - -
561A MET* 3.0 10.0 + - + +
562A ASP* 2.6 27.8 + - - +
563A ARG* 1.3 70.9 - - - +
565A ASN* 1.3 64.6 + - - +
566A GLU 2.6 10.4 + - - -
567A VAL* 3.2 15.4 + - - +
568A TYR* 2.7 64.2 + - + +
605A TYR* 6.0 1.1 - - - +
664A GLU* 4.3 1.8 - - - +
693A VAL* 4.0 25.6 - - + -
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Residues in contact with ASN 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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562A ASP 3.6 6.3 + - - +
563A ARG* 3.3 0.6 - - - -
564A VAL* 1.3 90.7 - - - +
566A GLU* 1.3 63.3 + - - +
568A TYR* 3.7 26.6 - - + +
569A GLU* 3.4 16.8 + - - +
605A TYR* 4.1 13.4 + - - -
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Residues in contact with GLU 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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559A VAL* 5.7 2.0 - - + -
563A ARG* 1.8 84.9 + - + +
564A VAL 2.6 1.6 - - - -
565A ASN* 1.3 77.9 - - - +
567A VAL* 1.3 69.6 + - + +
569A GLU* 3.0 14.8 + - - +
570A PHE* 3.2 9.6 + - - +
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Residues in contact with VAL 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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559A VAL* 4.2 15.9 - - + -
563A ARG 4.1 9.0 - - - +
564A VAL* 3.8 9.6 - - - +
566A GLU* 1.3 73.8 - - + +
568A TYR* 1.3 70.6 + - + +
570A PHE* 2.5 29.0 + - + +
571A VAL* 3.3 8.2 + - + +
660A VAL* 5.5 0.2 - - + -
662A VAL* 4.2 19.3 - - + -
691A PHE* 3.0 63.9 - - + -
693A VAL* 5.1 5.6 - - + -
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Residues in contact with TYR 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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564A VAL* 2.7 45.9 - - + +
565A ASN* 3.7 28.3 - - + +
567A VAL* 1.3 76.5 - - + +
569A GLU* 1.3 64.0 + - - +
571A VAL* 3.4 19.9 - - - +
572A ARG* 3.4 8.4 + - - +
583A ILE* 5.7 5.8 - - + -
602A MET* 4.6 8.3 - - - +
605A TYR* 4.2 17.5 + + - -
606A LEU* 4.5 26.7 - - + +
609A GLU* 3.5 31.5 - - + +
662A VAL* 5.6 6.5 - - + -
664A GLU* 3.0 24.4 + - - -
693A VAL* 5.3 1.6 - - + -
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Residues in contact with GLU 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 ASN 3.4 9.5 + - - +
566A GLU* 3.0 11.1 + - - +
567A VAL 2.6 4.2 + - - -
568A TYR* 1.3 72.5 - - - +
570A PHE* 1.3 54.0 + - - +
571A VAL 2.8 6.7 + - - -
572A ARG* 2.5 71.5 + - + +
573A GLN* 3.1 14.8 + - + +
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Residues in contact with PHE 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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566A GLU 3.2 3.7 + - - +
567A VAL* 2.5 23.9 + - + +
569A GLU* 1.3 74.0 - - - +
571A VAL* 1.3 56.6 + - + +
573A GLN* 3.2 10.8 - - + +
574A GLU* 3.0 42.6 + - + +
660A VAL* 3.7 20.2 - - + -
689A TYR* 4.1 31.0 - + - -
691A PHE* 3.2 42.2 - + + -
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Residues in contact with VAL 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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567A VAL* 3.8 14.8 - - + +
568A TYR* 3.4 15.9 - - - +
569A GLU 2.8 3.4 + - - -
570A PHE* 1.3 72.6 - - + +
572A ARG* 1.3 69.8 + - - +
573A GLN 2.6 2.0 + - - -
574A GLU* 4.3 4.7 - - + +
575A VAL* 2.5 48.5 + - + +
581A ALA* 3.7 24.2 - - + -
583A ILE* 6.3 2.7 - - + -
609A GLU* 4.7 9.0 - - - +
642A ILE* 4.6 7.0 - - + -
660A VAL* 4.0 21.3 - - + -
662A VAL* 5.3 5.6 - - + -
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Residues in contact with ARG 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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568A TYR* 3.4 4.4 + - - +
569A GLU* 2.5 54.0 + - - +
571A VAL* 1.3 77.6 - - - +
573A GLN* 1.3 53.2 + - - +
575A VAL* 3.6 6.2 - - - +
576A MET* 2.7 63.6 + - + +
608A LYS 3.4 10.1 + - - -
609A GLU* 3.4 53.8 + - - +
610A VAL* 4.2 3.6 - - - +
611A PHE* 4.4 13.4 - - - +
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Residues in contact with GLN 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 GLU* 3.1 14.9 + - + +
570A PHE* 3.2 17.9 - - + +
571A VAL 2.6 3.2 + - - -
572A ARG* 1.3 83.5 - - - +
574A GLU* 1.3 56.4 - - - +
575A VAL 2.1 21.7 + - - -
576A MET* 2.1 33.4 + - - +
577A ARG* 2.9 20.6 + - + +
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Residues in contact with GLU 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 PHE* 3.0 38.0 + - + +
571A VAL* 4.3 4.0 - - + +
573A GLN* 1.3 80.3 - - - +
575A VAL* 1.3 57.0 + - - +
577A ARG* 3.3 34.9 + - - +
578A GLY 3.4 1.6 + - - -
579A GLY* 3.1 19.9 + - - -
659A ASN* 4.1 32.2 + - + +
660A VAL* 5.3 6.3 - - + -
689A TYR* 4.4 16.5 + - + -
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Residues in contact with VAL 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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571A VAL* 2.5 37.0 + - + +
572A ARG* 3.6 11.4 - - - +
573A GLN 2.1 10.1 + - - -
574A GLU* 1.3 71.8 - - - +
576A MET* 1.3 71.1 + - - +
578A GLY* 3.3 9.0 + - - -
579A GLY 2.5 30.9 + - - +
580A GLN* 3.9 9.0 - - - -
611A PHE* 6.2 3.1 - - + -
641A ASP* 2.9 28.5 - - - +
642A ILE* 4.4 9.6 - - + -
657A ARG* 5.3 1.0 + - - -
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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