Contacts of the strand formed by residues 579 - 585 (chain A) in PDB entry 3DXE
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 579 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A TYR* 3.2 2.7 - - - -
547A TYR* 2.8 48.0 + - - -
577A GLN 3.9 6.9 + - - -
578A TRP* 1.3 70.8 - - - +
580A PRO* 1.3 72.4 - - + +
581A SER* 3.7 1.2 + - - -
594A HIS* 3.5 35.4 - - + +
601A LEU* 3.9 17.7 - - + -
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Residues in contact with PRO 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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544A GLN* 3.7 12.3 - - - +
545A VAL 3.6 7.4 - - - +
546A TYR* 3.8 15.0 - - + -
578A TRP 3.2 11.6 - - - +
579A THR* 1.3 93.0 - - + +
581A SER* 1.3 62.2 + - - +
594A HIS* 3.9 12.1 + - + -
595A GLN* 3.1 45.7 + - + +
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Residues in contact with SER 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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544A GLN* 3.5 9.8 + - - +
545A VAL* 2.9 33.4 + - - +
546A TYR 4.2 1.9 - - - -
547A TYR* 3.5 24.8 + - - +
579A THR 3.8 2.0 - - - -
580A PRO* 1.3 77.2 - - - +
582A HIS* 1.3 67.3 + - - +
592A ILE* 4.1 6.9 - - - +
593A LEU 3.0 21.5 - - - -
595A GLN* 3.8 5.8 - - - +
601A LEU* 4.2 12.3 - - - -
637A PHE* 4.9 1.0 - - - -
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Residues in contact with HIS 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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545A VAL* 4.7 7.0 - - + -
581A SER* 1.3 79.2 - - - +
583A VAL* 1.3 71.4 + - - +
584A SER* 5.3 2.9 - - - -
591A THR 3.7 0.9 - - - +
592A ILE* 3.9 1.4 - - - -
593A LEU* 3.0 60.5 + - + +
594A HIS 4.4 4.3 - - - -
595A GLN* 4.5 7.0 - - - -
598A GLU* 2.7 35.1 + - - -
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Residues in contact with VAL 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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545A VAL* 4.6 5.1 - - + +
581A SER* 5.5 0.2 - - - +
582A HIS* 1.3 83.1 + - - +
584A SER* 1.3 66.9 + - - +
585A VAL* 3.5 24.1 + - + +
590A LEU* 4.2 19.5 - - + -
591A THR 3.5 10.3 - - - +
592A ILE* 4.8 8.3 - - + +
623A PHE* 6.0 1.3 - - + -
637A PHE* 3.8 32.5 - - + -
646A LEU* 4.0 31.1 - - + +
650A VAL* 5.3 2.0 - - + -
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Residues in contact with SER 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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582A HIS* 4.0 4.1 + - - -
583A VAL* 1.3 71.4 - - - +
585A VAL* 1.3 59.9 + - - +
586A ALA* 5.9 0.9 - - - +
589A THR 3.7 1.9 - - - +
590A LEU* 3.4 4.3 - - - -
591A THR* 2.9 48.3 + - - -
593A LEU* 4.0 20.1 - - - +
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Residues in contact with VAL 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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583A VAL* 3.5 26.1 + - + +
584A SER* 1.3 76.4 + - - +
586A ALA* 1.3 64.1 + - - +
587A PRO* 4.9 0.3 - - - +
589A THR 4.1 1.1 - - - -
590A LEU* 3.8 20.0 - - + -
646A LEU* 4.4 5.8 - - + -
649A ALA* 3.7 41.1 - - + +
650A VAL* 4.4 6.7 - - + -
653A ALA* 3.8 11.0 - - + -
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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