Contacts of the strand formed by residues 599 - 607 (chain D) in PDB entry 2C11
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 599 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504C THR* 5.0 10.1 - - + +
505C GLY* 6.4 0.4 - - - -
508C GLY 4.8 1.6 - - - -
509C ASN* 3.4 32.9 + - + -
510C GLN* 2.8 38.2 + - - +
566D ARG* 5.6 4.0 + - - -
594D SER* 3.0 5.1 + - - -
595D ASN* 2.6 42.3 + - - +
597D TRP* 3.3 25.3 + - + -
598D GLY* 1.3 80.2 + - - +
600D PRO* 1.3 74.1 - - + +
709D ASN* 3.7 23.9 + - + +
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Residues in contact with PRO 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D TRP* 4.3 22.2 - - + +
588D TYR* 4.7 13.7 - - - +
590D ALA* 4.2 8.6 - - + +
591D SER 3.6 19.1 - - - +
592D ASN 5.1 3.4 - - - +
593D HIS 3.5 9.2 - - - +
594D SER* 4.0 5.1 - - - +
598D GLY 4.7 1.1 - - - +
599D HIS* 1.3 90.1 - - + +
601D ARG* 1.3 60.5 + - - +
602D GLY* 3.1 8.7 + - - -
708D TYR 3.8 0.9 - - - +
709D ASN* 3.8 14.2 + - - +
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Residues in contact with ARG 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D GLU* 2.8 31.9 + - - -
532D VAL* 3.2 11.8 - - - +
533D ALA* 3.4 24.4 - - + +
591D SER* 2.9 25.8 + - - +
593D HIS* 3.1 22.8 + - - +
594D SER 4.3 9.2 - - - -
595D ASN* 3.6 25.1 - - + +
600D PRO* 1.3 68.2 - - - +
602D GLY* 1.3 58.5 + - - +
709D ASN 3.3 9.9 - - - +
710D PHE* 2.9 48.9 + - + +
711D PHE* 5.4 0.8 - - - +
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Residues in contact with GLY 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532D VAL* 3.8 1.6 - - - -
588D TYR* 4.1 5.4 - - - -
589D LEU 3.1 13.0 - - - -
590D ALA* 3.3 10.3 - - - -
600D PRO 3.1 8.3 + - - -
601D ARG* 1.3 75.3 - - - +
603D TYR* 1.3 64.3 + - - -
604D ARG 4.2 0.2 - - - -
708D TYR* 2.9 33.7 + - - +
710D PHE* 3.5 10.0 - - - +
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Residues in contact with TYR 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D LEU* 3.7 25.2 - - + +
483D GLY* 2.5 28.3 + - - -
485D ILE* 5.2 1.1 - - + -
530D LEU* 4.5 18.2 - - + +
532D VAL* 4.0 17.7 - - + +
588D TYR* 3.1 13.8 - - - +
589D LEU* 2.7 21.0 + - - +
602D GLY* 1.3 73.0 - - - -
604D ARG* 1.3 62.4 + - - +
605D ILE* 3.9 4.9 + - - +
705D LEU* 3.4 31.9 - - + -
706D ARG 3.3 13.9 - - - -
707D PRO* 3.3 20.3 - - + +
710D PHE* 3.4 45.8 - + - -
711D PHE* 3.6 14.4 - - - -
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Residues in contact with ARG 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610C PHE* 6.2 2.4 - - - +
682C PHE* 6.4 0.4 - - - +
683C LEU 4.8 3.6 + - - -
699C ASN* 4.8 0.8 + - - -
585D ARG* 2.8 27.1 + - - +
586D TYR* 3.3 51.0 + - + -
587D LEU 3.4 13.0 - - - +
588D TYR* 3.3 12.7 - - + +
602D GLY 4.2 0.4 - - - -
603D TYR* 1.3 73.4 - - - +
605D ILE* 1.3 66.8 + - - +
606D GLN* 3.9 26.3 + - - +
704D PHE 3.2 5.2 - - - +
705D LEU* 3.4 4.2 - - - +
706D ARG* 2.6 80.9 + - + +
707D PRO 5.5 0.2 - - - +
708D TYR* 4.4 12.2 - - + +
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Residues in contact with ILE 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528D VAL* 5.6 1.1 - - + -
530D LEU* 4.9 6.3 - - + -
587D LEU* 2.9 28.0 + - + +
588D TYR* 5.2 1.8 - - - -
589D LEU* 4.7 16.6 - - + -
603D TYR 4.5 7.0 - - - +
604D ARG* 1.3 78.6 + - - +
606D GLN* 1.3 62.8 + - - +
607D MET* 4.0 25.8 + - + +
632D LEU* 4.5 20.8 - - + +
634D VAL* 5.6 0.9 - - + -
676D ALA* 3.6 30.3 - - + -
678D VAL* 4.4 14.8 - - + -
703D PHE* 4.9 5.4 - - + -
704D PHE 3.4 5.6 - - - +
705D LEU* 4.3 13.0 - - + -
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Residues in contact with GLN 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610C PHE* 3.7 38.0 - - + -
682C PHE* 6.3 0.8 - - - +
698C GLY 3.1 25.3 + - - +
699C ASN* 4.6 3.2 + - - -
604D ARG* 3.9 28.0 - - - +
605D ILE* 1.3 74.9 - - - +
607D MET* 1.3 63.9 + - - +
608D LEU* 4.8 3.6 - - + -
703D PHE* 3.0 5.4 - - - +
704D PHE* 2.6 53.6 + - + -
706D ARG* 3.3 28.4 + - - +
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Residues in contact with MET 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610C PHE* 3.5 18.4 - - - -
583D THR* 4.4 15.3 - - + +
587D LEU* 5.9 1.8 - - + -
605D ILE* 4.0 15.4 + - + +
606D GLN* 1.3 77.8 - - - +
608D LEU* 1.3 74.1 + - - +
609D SER* 3.8 11.2 - - - +
631D GLN* 3.6 48.0 - - + +
632D LEU* 4.1 22.0 - - + -
678D VAL* 4.0 20.2 - - + -
679D THR 5.3 2.0 - - - +
702D GLY 3.9 6.5 - - - +
703D PHE* 4.3 0.7 - - + -
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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