Contacts of the strand formed by residues 592 - 603 (chain A) in PDB entry 3K5M
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 LEU 592 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A LEU* 3.7 42.6 - - + +
419A ASP 3.7 4.3 - - - -
420A TYR* 3.6 38.6 - - + -
530A THR* 4.4 9.4 - - + -
549A THR* 5.8 0.2 - - - +
570A VAL* 3.6 30.4 - - + +
573A VAL* 3.7 35.2 - - + -
574A ASN* 2.8 34.5 + - - +
591A GLU* 1.3 73.9 - - - +
593A GLU* 1.3 60.2 + - - +
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Residues in contact with GLU 593 (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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418A LEU* 3.3 4.7 - - - -
419A ASP* 2.8 41.7 + - - +
421A LYS* 3.4 38.4 + - + +
481A LYS* 4.7 5.4 + - - -
570A VAL* 3.9 4.0 - - - -
591A GLU* 3.8 21.8 - - + +
592A LEU* 1.3 77.9 - - - +
594A TYR* 1.3 64.8 + - - +
595A GLU* 3.4 7.7 + - + +
914A DG3 4.6 8.8 + - - -
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Residues in contact with TYR 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 3.6 15.8 - - + +
417A VAL 4.1 0.9 - - - -
418A LEU* 3.5 20.9 - - + -
562A ALA 4.1 1.8 - - - -
563A ALA* 3.5 39.4 - - + +
566A GLY* 3.6 31.4 - - - +
567A ARG* 4.3 8.5 - - + -
570A VAL* 3.8 11.6 - - + +
593A GLU* 1.3 71.9 - - - +
595A GLU* 1.3 62.6 + - - +
596A THR* 3.5 24.0 - - - -
597A HIS* 3.2 25.3 + - - +
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Residues in contact with GLU 595 (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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417A VAL* 3.2 21.3 + - + +
419A ASP* 3.1 38.8 - - + +
593A GLU* 3.4 7.3 + - + +
594A TYR* 1.3 79.3 - - - +
596A THR* 1.3 74.7 + - - +
914A DG3 5.2 2.1 + - - -
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Residues in contact with THR 596 (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 LEU* 3.4 3.3 - - - -
417A VAL* 3.0 37.7 + - - +
594A TYR* 3.5 11.8 - - - -
595A GLU* 1.3 98.1 + - - +
597A HIS* 1.3 69.3 + - - +
598A PHE* 3.5 39.4 - - + -
621A ILE* 3.8 19.5 - - + +
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Residues in contact with HIS 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A SER* 3.4 36.0 - - - -
415A VAL 4.0 1.2 + - - -
416A LEU* 3.6 12.8 - - + +
557A HIS 3.7 12.3 + - - -
559A GLU* 2.9 47.2 + - - +
562A ALA* 3.5 23.9 - - + +
594A TYR* 3.2 22.5 + - - +
596A THR* 1.3 79.6 - - - +
598A PHE* 1.3 61.5 + - - +
599A CYS* 3.5 17.8 + - - +
620A LEU 4.3 0.5 - - - +
621A ILE* 4.0 17.1 - - - +
622A GLN 5.1 0.2 + - - -
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Residues in contact with PHE 598 (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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414A SER* 3.2 1.4 + - - -
415A VAL* 2.7 39.4 + - + +
417A VAL* 3.9 21.8 - - + -
596A THR* 3.5 23.6 - - + -
597A HIS* 1.3 72.1 - - - +
599A CYS* 1.3 65.7 + - - +
600A ARG* 3.1 11.4 + - - +
601A PHE* 3.7 33.9 - + + -
617A TYR* 4.8 10.3 - + - -
619A GLY* 3.6 29.6 - - - -
620A LEU 3.6 1.6 - - - -
621A ILE* 3.4 33.2 - - + -
630A VAL* 3.9 25.6 - - + -
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Residues in contact with CYS 599 (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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413A ASP* 2.9 10.7 - - - +
414A SER* 2.6 20.8 + - - +
557A HIS 5.8 1.1 - - - +
559A GLU* 4.1 16.8 - - - +
597A HIS* 3.5 17.7 + - - +
598A PHE* 1.3 71.4 - - - +
600A ARG* 1.3 72.5 + - + +
620A LEU* 3.1 48.1 + - - -
622A GLN* 4.6 16.8 - - + +
627A GLN* 5.3 2.0 - - - -
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Residues in contact with ARG 600 (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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411A LEU* 3.5 37.5 + - - +
412A TYR* 3.2 18.0 + - - +
413A ASP* 2.7 38.2 + - - -
598A PHE* 3.7 3.5 - - - +
599A CYS* 1.3 93.3 - - + +
601A PHE* 1.3 61.2 + - - +
619A GLY* 3.2 2.6 - - - -
620A LEU* 2.9 32.0 + - + -
656A ILE 3.6 9.1 + - - -
657A PHE* 3.1 47.1 + - + +
659A ASN* 3.2 31.0 + - - +
768A ILE* 6.1 0.2 - - - +
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Residues in contact with PHE 601 (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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410A GLY 3.5 0.3 - - - +
411A LEU* 3.6 4.0 - - - +
412A TYR* 2.9 45.1 + + - -
415A VAL* 3.4 38.8 - - + -
542A ILE* 3.6 23.8 - - + -
550A PHE* 3.8 20.6 - + + -
598A PHE* 3.7 29.6 - + + +
600A ARG* 1.3 75.1 - - - +
602A LEU* 1.3 60.2 + - - +
603A MET* 3.7 33.9 - - + -
617A TYR* 3.5 31.4 - + + -
618A ALA 3.5 11.4 - - - -
619A GLY* 4.3 0.2 - - - -
657A PHE* 4.5 0.6 - - - -
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Residues in contact with LEU 602 (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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410A GLY 3.7 6.7 - - - +
411A LEU* 4.1 12.8 - - + -
601A PHE* 1.3 77.5 - - - +
603A MET* 1.3 60.4 + - - +
604A PRO* 3.2 19.0 - - + +
617A TYR* 3.4 5.7 - - - +
618A ALA* 2.7 33.3 + - + +
634A LEU* 5.6 1.1 - - + -
653A TYR* 3.1 41.7 - - + +
657A PHE* 4.1 11.4 - - + -
763A GLY 4.6 3.8 - - - +
764A ILE* 3.4 24.7 - - + -
767A PHE* 4.0 33.4 - - + -
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Residues in contact with MET 603 (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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407A SER* 3.4 31.0 - - - +
408A ARG 3.3 26.7 - - - +
409A PRO* 3.1 7.4 - - + +
410A GLY 2.6 40.9 + - - +
412A TYR* 4.1 4.0 - - + -
542A ILE* 5.0 1.8 - - + -
543A TYR* 4.0 24.0 - - + -
601A PHE* 3.7 24.8 + - + -
602A LEU* 1.3 70.8 - - - +
604A PRO* 1.3 68.6 - - - +
613A SER 3.5 14.1 - - - +
616A ARG 4.0 2.7 - - - +
617A TYR* 3.6 25.1 - - + -
767A PHE* 3.4 4.1 - - - -
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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