Contacts of the helix formed by residues 600 - 610 (chain B) in PDB entry 3U11
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 ASP 600 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599B ALA* 1.3 71.0 - - - +
601B PRO* 1.4 76.3 - - - +
602B ASN* 3.8 20.9 - - - +
603B PHE* 3.1 21.2 + - + +
604B VAL* 3.0 22.6 + - - +
696B TYR* 4.8 6.4 + - - -
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Residues in contact with PRO 601 (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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583B ASN* 5.5 0.3 - - - +
599B ALA 3.4 8.5 - - - +
600B ASP* 1.4 93.0 - - - +
602B ASN* 1.3 63.1 + - - +
604B VAL* 3.8 7.8 - - + +
605B THR* 3.0 33.8 + - - +
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Residues in contact with ASN 602 (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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600B ASP* 3.3 16.0 + - - +
601B PRO* 1.3 81.1 - - - +
603B PHE* 1.3 56.6 + - - +
605B THR* 3.9 5.1 - - - +
606B SER* 3.0 30.7 + - - -
696B TYR* 3.9 8.6 + - - +
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Residues in contact with PHE 603 (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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595B LEU 3.8 20.6 - - - -
596B PHE* 4.1 12.3 - + - -
599B ALA* 4.5 8.3 - - + -
600B ASP* 3.1 23.8 + - + +
602B ASN* 1.3 76.5 - - - +
604B VAL* 1.3 72.1 + - + +
606B SER* 3.3 4.1 - - - -
607B MET* 3.1 40.7 + - + +
692B VAL* 4.5 0.4 - - + -
696B TYR* 3.4 58.3 + + + +
698B MET* 6.0 1.6 - - + -
699B MET* 3.7 37.5 - - + -
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Residues in contact with VAL 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B ASN* 4.0 8.5 - - - +
590B VAL* 3.7 33.7 - - + -
596B PHE* 3.4 36.6 - - + +
599B ALA* 3.9 13.7 - - + +
600B ASP 3.0 20.5 + - - +
601B PRO* 3.8 9.4 - - + +
603B PHE* 1.3 79.3 - - + +
605B THR* 1.3 52.1 + - - +
607B MET* 3.0 8.4 + - - +
608B LEU* 2.8 45.2 + - + +
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Residues in contact with THR 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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579B GLU* 3.6 44.9 - - + +
582B ILE* 5.6 1.1 - - + -
583B ASN* 2.9 27.0 + - - +
601B PRO* 3.0 20.2 + - - +
602B ASN* 3.9 6.3 - - - -
604B VAL* 1.3 71.8 - - - +
606B SER* 1.3 60.1 - - - +
608B LEU* 4.3 4.7 - - - +
609B THR* 2.8 42.0 + - + +
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Residues in contact with SER 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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602B ASN 3.0 20.3 + - - -
603B PHE* 3.3 9.9 - - - -
605B THR* 1.3 75.7 - - - +
607B MET* 1.3 63.4 + - - +
609B THR* 3.4 11.0 + - - -
610B LYS* 3.1 37.4 + - - +
692B VAL* 4.7 4.0 - - - +
695B GLU* 4.1 8.1 + - - -
696B TYR* 3.9 19.7 - - - -
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Residues in contact with MET 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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595B LEU* 4.9 0.4 - - + -
596B PHE* 3.9 34.3 - - + -
603B PHE* 3.1 39.0 + - + +
604B VAL 3.0 8.7 + - - +
606B SER* 1.3 76.0 - - - +
608B LEU* 1.3 65.9 + - - +
610B LYS* 3.1 18.2 + - - +
611B LEU* 3.4 17.4 - - + +
634B PHE* 3.9 22.0 - - + -
684B LEU* 4.4 19.0 - - + +
692B VAL* 3.7 31.4 - - + -
699B MET* 4.4 14.8 - - + -
703B PHE* 5.3 2.9 - - + -
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Residues in contact with LEU 608 (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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582B ILE* 3.6 19.3 - - + +
583B ASN* 3.6 37.0 - - - +
586B CSO 3.9 33.1 + - + +
589B LEU* 4.6 2.5 - - + -
590B VAL* 3.9 24.7 - - + -
596B PHE* 4.5 12.8 - - + -
604B VAL* 2.8 24.9 + - + +
605B THR 3.1 2.7 + - - +
607B MET* 1.3 73.6 - - - +
609B THR* 1.3 62.4 + - - +
610B LYS 3.1 1.2 + - - -
611B LEU* 3.1 41.5 + - + +
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Residues in contact with THR 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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575B GLU* 5.8 0.4 - - - +
578B ARG* 5.9 3.8 - - + -
579B GLU* 4.8 10.8 - - + +
582B ILE* 4.5 25.4 - - + -
605B THR* 2.8 37.0 + - + +
606B SER* 3.4 15.1 + - - -
608B LEU* 1.3 71.4 - - - +
610B LYS* 1.3 64.4 + - - +
611B LEU 4.4 0.9 - - - +
612B ARG* 3.1 18.5 + - - -
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Residues in contact with LYS 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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606B SER* 3.1 29.2 + - - +
607B MET* 3.1 8.4 + - - +
608B LEU 3.1 1.2 - - - -
609B THR* 1.3 84.0 + - - +
611B LEU* 1.3 61.2 + - - +
612B ARG* 3.5 19.7 + - - +
683B SER 4.0 4.7 - - - +
684B LEU* 3.8 19.4 - - + +
685B SER 4.9 0.5 + - - -
688B ASN* 3.7 32.3 + - - +
691B GLU* 3.7 34.5 + - - -
692B VAL* 3.3 33.4 - - + -
695B GLU* 4.6 4.7 + - - -
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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