Contacts of the strand formed by residues 618 - 630 (chain A) in PDB entry 3E20
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 LYS 618 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563A GLN* 6.4 0.9 - - - +
564A ILE 3.8 5.2 - - - -
565A ALA* 4.6 15.9 - - + +
598A LYS* 3.6 9.2 - - - +
599A LEU* 3.0 42.8 + - + +
600A ASP 2.0 35.3 + - - -
601A LYS* 3.7 12.1 + - - +
603A ASN* 3.3 21.5 + - - +
616A GLY 5.6 3.4 - - - +
617A MET* 1.3 75.6 - - - +
619A ILE* 1.3 62.4 + - - +
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Residues in contact with ILE 619 (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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563A GLN* 3.6 2.1 - - - -
564A ILE* 2.7 37.2 + - + +
566A ILE* 3.1 35.4 - - + -
573A LEU* 5.8 0.7 - - + -
592A PHE* 4.9 8.1 - - + -
595A LEU* 4.1 22.2 - - + -
597A HIS 3.1 17.9 - - - +
598A LYS* 4.6 1.8 - - - -
599A LEU* 3.3 9.1 - - - +
610A PRO* 4.6 6.7 - - + -
613A ALA* 4.6 7.9 - - + -
617A MET* 3.8 8.5 - - + +
618A LYS* 1.3 78.1 - - - +
620A ILE* 1.3 72.0 + - - +
621A ALA* 3.6 28.3 - - + +
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Residues in contact with ILE 620 (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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561A ILE* 3.8 25.4 - - + -
562A ALA 3.5 11.2 - - - +
563A GLN* 4.3 11.2 - - + +
596A LEU* 2.8 26.1 + - + +
597A HIS* 3.1 50.3 + - + +
599A LEU* 4.1 14.8 - - + -
605A LYS* 4.9 11.7 - - + +
619A ILE* 1.3 80.6 - - - +
621A ALA* 1.3 59.5 + - - +
658A VAL* 4.8 9.2 - - + -
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Residues in contact with ALA 621 (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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561A ILE* 3.2 10.6 - - - +
562A ALA 3.1 31.1 + - - +
564A ILE* 4.7 1.6 - - + -
592A PHE* 3.8 26.9 - - + -
594A LYS 3.1 14.8 - - - +
595A LEU* 3.9 4.7 - - + -
596A LEU* 4.0 3.6 - - - +
619A ILE* 3.6 18.9 - - + +
620A ILE* 1.3 74.3 - - - +
622A GLU* 1.3 62.0 + - - +
623A LEU* 4.2 4.8 - - + +
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Residues in contact with GLU 622 (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 ARG* 2.8 35.5 + - - -
560A PHE 3.5 9.4 - - - +
561A ILE* 4.3 10.8 - - + +
592A PHE* 3.6 0.3 - - - -
593A ALA* 2.5 42.9 + - + +
594A LYS* 2.7 59.7 + - + +
596A LEU* 4.7 8.1 - - + +
621A ALA* 1.3 72.9 - - - +
623A LEU* 1.3 65.5 + - - +
661A LEU* 4.3 16.1 - - + +
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Residues in contact with LEU 623 (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 THR 3.5 0.9 - - - +
559A ARG* 3.3 5.9 - - - +
560A PHE* 2.7 73.8 + - + +
562A ALA* 4.9 2.2 - - + -
564A ILE* 3.9 22.4 - - + -
581A MET* 4.4 1.1 - - + -
590A VAL* 3.8 17.0 - - + -
591A SER 3.6 4.3 - - - +
592A PHE* 3.5 37.5 - - + -
621A ALA* 4.2 5.4 - - + +
622A GLU* 1.3 87.7 - - - +
624A GLU* 1.3 63.4 + - - +
643A PHE* 4.1 13.0 - - + -
645A LEU* 4.8 7.2 - - + -
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Residues in contact with GLU 624 (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 THR 3.0 4.5 - - - +
559A ARG* 3.7 45.5 + - + +
590A VAL* 3.3 3.6 - - - +
591A SER* 2.8 44.5 + - - +
593A ALA* 3.4 27.6 - - + +
594A LYS* 5.3 1.4 + - - -
622A GLU* 4.3 0.2 - - - +
623A LEU* 1.3 77.0 - - - +
625A THR* 1.3 64.9 + - - +
626A GLN* 5.9 0.2 + - - -
403B LYS* 4.5 16.0 + - - -
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Residues in contact with THR 625 (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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557A THR 3.8 0.4 + - - +
558A THR* 2.9 34.5 + - - +
560A PHE* 4.6 11.2 - - + -
581A MET* 5.0 4.7 - - - -
588A GLU* 4.6 5.4 - - + -
589A GLU* 3.7 17.3 - - - +
590A VAL* 3.8 14.4 - - + -
624A GLU* 1.3 81.2 - - - +
626A GLN* 1.3 67.6 + - - +
627A THR 2.9 21.5 + - - -
629A VAL* 3.8 20.9 - - + +
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Residues in contact with GLN 626 (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 THR* 4.3 3.8 - - - +
588A GLU* 5.1 4.2 + - - +
589A GLU* 3.5 41.0 + - + -
591A SER* 5.8 1.8 + - - -
624A GLU 5.9 0.4 + - - -
625A THR* 1.3 75.7 - - - +
627A THR* 1.3 72.8 + - + +
628A PRO* 4.9 0.2 - - - +
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Residues in contact with THR 627 (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 THR* 3.5 5.6 - - - -
588A GLU* 3.7 22.9 + - - +
625A THR* 2.9 17.7 + - - -
626A GLN* 1.3 87.1 - - + +
628A PRO* 1.3 82.6 + - + +
629A VAL* 3.4 4.0 + - - +
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Residues in contact with PRO 628 (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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503A PRO* 3.6 36.9 - - + +
545A TYR* 5.2 3.8 - - - -
556A ALA* 4.6 1.8 - - + -
557A THR* 3.6 19.1 - - - +
558A THR* 3.5 13.0 - - + -
588A GLU* 5.8 0.5 - - - +
626A GLN 4.9 0.2 - - - +
627A THR* 1.3 95.8 + - + +
629A VAL* 1.3 60.2 + - - +
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Residues in contact with VAL 629 (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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503A PRO* 5.0 1.3 - - - -
556A ALA* 3.5 4.4 - - - -
557A THR 3.2 23.8 + - - +
581A MET* 5.4 2.2 - - - -
583A ILE* 4.7 12.8 - - + -
584A HIS* 5.0 6.3 - - - +
586A ALA* 5.1 9.0 - - + -
588A GLU* 4.2 18.8 - - + +
625A THR* 3.8 26.0 - - + +
627A THR 3.6 10.3 - - - +
628A PRO* 1.3 76.5 - - - +
630A CYS* 1.3 78.3 + - - +
631A MET* 3.6 23.0 + - + +
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Residues in contact with CYS 630 (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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502A MET* 3.5 46.4 - - - -
503A PRO* 3.6 8.5 - - - -
544A GLY 5.2 1.1 - - - -
545A TYR* 4.8 1.6 - - - -
546A VAL* 3.6 30.1 - - + -
554A VAL* 4.1 9.9 - - + -
555A HIS 3.2 13.9 - - - +
556A ALA* 3.9 4.3 - - - -
583A ILE* 4.6 0.2 - - - +
584A HIS* 3.0 25.7 + - + -
629A VAL* 1.3 78.5 - - - +
631A MET* 1.3 63.0 + - - +
640A MET* 4.9 0.4 - - - -
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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