Contacts of the helix formed by residues 603 - 615 (chain B) in PDB entry 2AN3
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 603 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527B TYR* 3.3 32.5 - - + +
528B GLN* 3.8 26.5 - - - +
530B PHE* 3.5 29.2 - - + +
601B ASP* 3.1 10.9 + - - +
602B PHE* 1.3 91.8 - - + +
604B GLU* 1.3 63.7 + - - +
605B VAL* 4.0 18.8 - - + -
606B ASN* 3.5 3.4 + - - +
607B ARG* 3.3 26.2 + - - +
2002B SAH 3.4 18.2 - - - +
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Residues in contact with GLU 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B PHE 4.0 1.4 + - - -
603B LEU* 1.3 70.4 - - - +
605B VAL* 1.3 61.3 + - + +
606B ASN 3.1 0.2 - - - -
607B ARG* 3.1 28.9 + - + +
608B GLN* 2.8 51.1 + - + +
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Residues in contact with VAL 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B PHE 4.4 9.0 - - - +
532B PRO* 3.9 29.7 - - + +
603B LEU* 4.0 22.0 - - + -
604B GLU* 1.3 78.5 - - + +
606B ASN* 1.3 59.7 + - - +
608B GLN* 3.4 18.8 + - - +
609B GLU* 3.0 26.9 + - - +
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Residues in contact with ASN 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B PHE* 3.4 19.7 - - - -
532B PRO* 3.2 21.0 - - - +
581B GLY 3.7 12.0 - - - +
582B PRO* 3.2 23.1 - - - +
601B ASP* 2.9 21.3 + - - +
603B LEU* 3.5 6.5 + - - +
604B GLU 3.1 0.6 - - - -
605B VAL* 1.3 78.4 - - - +
607B ARG* 1.3 67.7 + - - +
609B GLU* 3.0 6.7 + - - +
610B LEU* 2.9 25.5 + - - +
2002B SAH 2.8 32.1 + - - -
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Residues in contact with ARG 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B ASP* 2.7 40.4 + - + -
602B PHE 3.5 15.4 + - - -
603B LEU 3.3 13.8 + - - +
604B GLU* 3.1 35.5 + - + +
606B ASN* 1.3 76.9 - - - +
608B GLN* 1.3 57.3 + - + +
610B LEU* 3.3 6.0 + - - +
611B GLY* 2.9 23.9 + - - -
654B VAL* 3.6 33.8 + - + +
655B LEU 3.6 22.4 - - - -
656B PRO* 3.4 28.7 - - - +
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Residues in contact with GLN 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B GLU* 2.8 36.8 + - + +
605B VAL* 3.6 27.0 + - - +
607B ARG* 1.3 76.3 - - + +
609B GLU* 1.3 59.1 + - - +
611B GLY* 3.3 2.6 + - - +
612B ARG* 3.0 37.7 + - + +
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Residues in contact with GLU 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B PRO* 4.1 16.3 - - + +
533B ARG* 2.5 44.3 + - - +
536B LEU* 4.3 8.2 - - + +
582B PRO* 3.6 28.7 - - + +
605B VAL 3.0 13.8 + - - +
606B ASN* 3.0 9.6 + - - +
608B GLN* 1.3 76.4 - - - +
610B LEU* 1.3 64.4 + - - +
612B ARG* 3.2 36.0 + - - +
613B TRP* 3.3 12.0 + - - +
620B ALA* 4.5 1.9 - - - +
621B PHE* 4.2 6.3 + - + -
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Residues in contact with LEU 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B SER* 4.1 7.9 - - - -
581B GLY 3.3 20.6 - - - +
582B PRO* 3.7 17.7 - - + +
583B THR 3.6 22.2 - - - +
584B VAL* 3.8 11.9 - - + -
599B MET* 3.8 31.9 - - + -
600B THR 5.2 2.5 - - - +
601B ASP* 5.7 0.4 - - + -
606B ASN 2.9 10.7 + - - +
607B ARG* 3.6 8.7 - - + +
609B GLU* 1.3 74.0 - - - +
611B GLY* 1.3 55.3 + - - +
613B TRP* 3.0 9.0 + - + +
614B LEU* 2.7 39.4 + - + +
654B VAL* 4.2 26.0 - - + -
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Residues in contact with GLY 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B ARG 2.9 15.6 + - - -
608B GLN* 3.3 5.6 + - - -
609B GLU 3.3 0.2 - - - -
610B LEU* 1.3 78.2 - - - +
612B ARG* 1.3 59.9 + - - +
614B LEU* 3.3 14.0 + - - +
615B GLN* 3.0 38.7 + - - +
654B VAL* 5.5 0.9 - - - +
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Residues in contact with ARG 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B ARG* 3.2 28.1 - - - +
608B GLN* 3.0 26.8 + - + +
609B GLU* 3.2 34.2 + - - +
610B LEU 3.1 0.4 - - - -
611B GLY* 1.3 77.4 - - - +
613B TRP* 1.3 62.2 + - - +
615B GLN* 3.3 6.3 + - - +
616B GLU 3.3 2.9 + - - -
617B GLU* 3.0 52.3 + - - +
619B GLY* 3.7 16.4 + - - -
620B ALA* 3.7 12.2 - - + +
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Residues in contact with TRP 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B VAL* 3.9 25.6 - - + -
588B LEU* 5.8 0.7 - - + -
599B MET* 6.4 0.2 - - - -
609B GLU 3.3 7.8 + - - +
610B LEU* 3.0 10.8 + - + +
612B ARG* 1.3 79.0 - - - +
614B LEU* 1.3 77.2 + - + +
616B GLU* 2.9 7.5 + - - +
620B ALA* 3.6 12.7 - - + +
621B PHE* 3.4 25.5 + - + +
623B TRP* 3.7 27.3 - + + +
627B SER* 5.4 0.4 - - - -
644B GLU* 3.8 32.5 + - + -
647B LEU* 3.7 35.7 - - + -
648B ARG* 2.9 74.5 + - + +
651B VAL* 5.7 0.7 - - + -
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Residues in contact with LEU 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599B MET* 5.6 3.8 - - - -
610B LEU* 2.7 24.8 + - + +
611B GLY* 3.6 12.3 - - - +
612B ARG 3.3 0.2 - - - -
613B TRP* 1.3 86.4 - - + +
615B GLN* 1.3 61.1 + - + +
616B GLU* 3.3 1.2 + - - +
648B ARG* 3.5 40.6 - - - +
651B VAL* 4.1 33.0 - - + +
654B VAL* 4.0 27.4 - - + -
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Residues in contact with GLN 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B GLY* 3.0 29.2 + - - +
612B ARG* 4.1 2.4 - - - +
613B TRP 3.1 0.4 - - - -
614B LEU* 1.3 77.4 - - + +
616B GLU* 1.3 71.2 + - - +
617B GLU* 3.1 36.7 + - + +
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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