Contacts of the helix formed by residues 577 - 585 (chain A) in PDB entry 6WLY
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 PRO 577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A GLU* 4.1 9.2 - - - +
419A ALA* 5.2 0.9 - - - -
575A ALA 4.8 0.4 - - - +
576A GLY* 1.3 86.1 - - - +
578A PRO* 1.3 74.9 - - + +
579A ALA* 4.1 14.6 - - + +
580A SER* 2.7 32.2 + - - +
581A ILE* 4.1 1.7 + - - +
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Residues in contact with PRO 578 (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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419A ALA* 6.0 0.7 - - + -
451A ASP* 3.3 17.5 - - - +
452A GLY* 3.4 35.0 - - - +
453A ARG* 3.8 18.6 - - + +
576A GLY 4.6 0.9 - - - +
577A PRO* 1.3 86.2 - - + +
579A ALA* 1.3 60.6 + - - +
581A ILE* 2.9 16.9 + - + +
582A VAL 3.5 0.9 + - - -
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Residues in contact with ALA 579 (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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451A ASP 3.9 2.4 + - - -
577A PRO* 3.0 13.8 + - + +
578A PRO* 1.3 78.5 - - - +
580A SER* 1.3 60.3 + - - +
582A VAL* 3.2 24.5 + - + +
583A PRO* 3.4 9.5 - - - +
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Residues in contact with SER 580 (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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415A GLU* 4.1 28.0 + - - +
416A GLN* 2.9 34.1 + - - +
419A ALA* 4.7 0.3 - - - +
576A GLY* 3.8 10.6 + - - -
577A PRO* 2.7 28.6 + - - +
579A ALA* 1.3 78.0 - - - +
581A ILE* 1.3 65.5 + - - +
583A PRO* 3.5 8.3 - - - +
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Residues in contact with ILE 581 (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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403A LEU* 6.2 0.7 - - + -
406A ILE* 4.9 0.9 - - + -
412A MET* 4.8 0.2 - - + -
416A GLN* 3.5 45.3 - - + +
419A ALA* 4.2 11.4 - - + -
420A VAL* 4.2 12.1 - - + -
448A LEU* 3.5 31.0 - - + -
452A GLY* 3.9 17.5 - - - +
454A VAL* 4.9 7.2 - - + -
577A PRO 4.5 1.8 - - - +
578A PRO* 2.9 12.0 + - + +
580A SER* 1.3 82.3 - - - +
582A VAL* 1.3 65.8 + - - +
583A PRO* 3.3 1.3 - - - -
584A LEU* 2.9 31.8 + - + +
585A MET* 4.1 3.0 + - - +
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Residues in contact with VAL 582 (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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450A HIS 3.6 12.8 - - - +
451A ASP* 3.4 37.2 - - - +
578A PRO 3.9 0.9 - - - +
579A ALA* 3.2 19.3 + - + +
581A ILE* 1.3 76.8 - - - +
583A PRO* 1.3 65.6 - - + +
584A LEU 3.0 1.6 + - - -
585A MET* 3.2 18.4 + - - +
588A ASN* 3.1 37.2 + - - +
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Residues in contact with PRO 583 (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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416A GLN* 4.4 7.4 - - - +
579A ALA 3.4 13.5 - - - +
580A SER* 3.5 13.7 - - - +
581A ILE 3.4 4.0 - - - -
582A VAL* 1.3 92.2 - - + +
584A LEU* 1.3 60.4 + - + +
585A MET 3.3 0.7 + - - -
588A ASN* 4.2 11.3 - - + +
589A ARG* 3.6 24.1 + - - +
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Residues in contact with LEU 584 (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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406A ILE* 3.6 31.2 - - + +
410A THR* 4.1 11.6 + - - +
411A ARG 4.0 16.6 - - - +
412A MET* 4.0 20.9 - - + -
416A GLN* 3.5 49.6 - - + +
581A ILE* 2.9 28.2 + - + +
583A PRO* 1.3 77.4 - - + +
585A MET* 1.3 58.7 + - - +
589A ARG* 2.8 30.2 + - - +
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Residues in contact with MET 585 (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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400A GLY* 3.4 40.8 - - - +
406A ILE* 4.2 6.7 - - + -
448A LEU* 4.1 21.5 - - + -
449A THR 3.5 11.4 - - - +
450A HIS 3.2 27.8 - - - +
452A GLY* 4.2 5.2 - - - +
581A ILE 4.5 2.5 - - - +
582A VAL* 3.2 31.8 + - + +
584A LEU* 1.3 78.8 - - - +
586A ARG* 1.3 67.9 + - - +
587A GLN* 3.3 23.1 - - - +
588A ASN* 2.9 13.6 + - - +
589A ARG* 3.1 14.0 + - - +
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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