Contacts of the strand formed by residues 600 - 606 (chain A) in PDB entry 3I7N
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 HIS 600 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A LEU* 2.9 31.9 - - + +
547A GLY* 4.3 11.0 - - - -
594A THR 3.3 7.2 - - - +
595A THR* 2.9 24.0 + - + +
598A SER 5.7 0.2 - - - -
599A SER* 1.3 82.7 + - - +
601A TYR* 1.3 55.4 + - - +
615A GLY* 3.7 3.3 - - - -
616A LEU* 2.8 49.1 + - + +
617A ASN* 5.7 0.4 - - - -
618A ILE* 3.2 54.7 - - + +
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Residues in contact with TYR 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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592A LEU 3.2 0.7 - - - +
593A MET* 2.9 10.0 - - - +
594A THR* 2.8 48.7 + - - +
595A THR* 4.1 2.7 - - - -
596A PHE* 3.0 42.1 - + + +
597A GLU* 4.4 0.3 + - - -
599A SER* 3.2 41.3 - - - -
600A HIS* 1.3 74.8 - - - +
602A LEU* 1.3 60.9 + - - +
603A LEU* 4.6 8.1 - - + -
614A PHE 4.1 8.7 - - - +
615A GLY* 4.3 3.1 - - - -
616A LEU* 4.5 2.4 - - - +
664A HIS* 2.8 38.0 + + - -
665A LYS* 3.9 3.6 + - - -
666A LEU* 3.7 34.2 - - + +
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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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557A ALA* 3.9 18.8 - - + -
566A ALA* 5.6 5.2 - - + -
568A ILE* 4.4 20.0 - - + -
591A ILE* 3.7 35.9 - - + -
592A LEU 2.9 8.7 - - - +
593A MET* 5.3 1.8 - - + -
601A TYR* 1.3 73.2 - - - +
603A LEU* 1.3 62.6 + - - +
604A CYS* 5.6 1.1 - - + -
614A PHE* 2.5 74.0 + - + +
615A GLY* 4.0 4.6 - - - +
616A LEU* 4.3 19.1 - - + +
622A LEU 5.3 3.8 - - - +
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Residues in contact with LEU 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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591A ILE* 3.4 5.5 - - - +
592A LEU* 2.8 54.8 + - + +
594A THR* 4.0 19.7 - - - +
601A TYR* 4.6 6.1 - - + -
602A LEU* 1.3 80.8 - - - +
604A CYS* 1.3 63.3 + - - +
611A LEU* 4.2 16.8 - - + -
612A PHE 3.8 9.2 - - - +
613A TYR* 4.6 10.1 - - + +
614A PHE* 5.1 2.0 - - - +
638A LEU* 4.3 12.8 - - + -
649A VAL* 4.8 9.4 - - + -
659A ILE* 4.3 31.4 - - + -
666A LEU* 5.1 11.0 - - + -
668A PHE* 5.5 2.5 - - + -
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Residues in contact with CYS 604 (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 ALA* 4.6 6.3 - - + -
582A LEU* 4.0 20.0 - - + -
588A PRO* 3.6 32.3 - - - -
590A SER 3.2 9.6 - - - -
591A ILE* 3.8 20.6 - - + -
602A LEU* 5.6 1.3 - - + -
603A LEU* 1.3 77.7 - - - +
605A ALA* 1.3 60.7 + - - +
606A LEU* 3.8 4.9 + - - +
611A LEU* 3.7 4.8 - - - +
612A PHE* 3.1 39.6 + - + +
614A PHE* 6.1 3.6 - - + -
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Residues in contact with ALA 605 (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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588A PRO* 3.5 4.5 - - - +
589A ARG* 2.8 22.5 + - + -
590A SER* 2.7 21.4 + - - +
604A CYS* 1.3 72.1 - - - +
606A LEU* 1.3 61.0 + - - +
610A ALA 3.9 5.8 - - - +
611A LEU* 4.4 7.2 - - + -
636A THR* 3.3 44.9 - - + +
638A LEU* 4.1 11.8 - - + +
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Residues in contact with LEU 606 (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 ILE* 5.1 2.0 - - + -
582A LEU* 3.9 22.4 - - + -
583A GLY 5.6 3.1 - - - +
586A ILE* 4.2 14.6 - - + +
587A ILE 4.0 4.7 - - - +
588A PRO* 3.4 34.8 - - + -
589A ARG* 4.1 4.9 - - - +
604A CYS* 4.2 3.4 - - - +
605A ALA* 1.3 76.8 - - - +
607A GLY* 1.3 61.7 + - - +
608A ASP* 3.1 30.4 + - - +
609A GLY* 3.3 10.9 + - - -
610A ALA* 3.1 11.6 + - + +
612A PHE* 3.4 35.7 - - + -
628A LYS* 6.1 0.4 - - - -
635A PRO* 3.7 9.7 - - - +
636A THR* 4.1 2.9 + - - -
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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