Contacts of the strand formed by residues 586 - 595 (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 TYR 586 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683C LEU* 3.4 35.1 + - + -
684C HIS* 3.7 10.7 - - - -
685C ILE* 3.3 46.6 + - + -
687C HIS* 4.5 2.0 + + - -
1747C CU 4.0 6.6 - - - -
540D TRP 3.9 0.3 - - - +
541D ALA* 3.4 2.6 - - - -
542D GLU* 2.7 55.3 + - + +
584D PRO* 3.8 2.2 - - - +
585D ARG* 1.3 80.6 - - + +
587D LEU* 1.3 60.7 + - - +
588D TYR* 4.3 5.1 - + + -
604D ARG* 3.3 50.1 + - + +
706D ARG* 4.5 0.2 + - - -
708D TYR* 3.4 34.8 - + - -
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Residues in contact with LEU 587 (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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539D VAL* 3.7 22.4 - - + -
540D TRP 3.1 19.7 - - - +
541D ALA* 3.9 0.2 - - + -
569D LEU* 3.9 9.0 - - + -
577D PHE* 4.1 15.7 - - + -
583D THR* 5.6 3.6 - - - -
584D PRO* 3.6 34.3 + - + +
585D ARG 4.0 1.6 + - - -
586D TYR* 1.3 75.8 - - - +
588D TYR* 1.3 65.7 + - - +
589D LEU* 6.1 1.1 - - + -
604D ARG* 3.4 6.9 - - - +
605D ILE* 2.9 36.9 + - + +
607D MET* 5.9 2.0 - - + -
632D LEU* 3.5 32.1 - - + -
634D VAL* 5.7 2.2 - - + -
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Residues in contact with TYR 588 (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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539D VAL* 3.5 2.4 - - - +
540D TRP* 2.9 77.9 + + + +
542D GLU* 3.3 38.6 + - + +
566D ARG* 4.8 2.3 + - - -
586D TYR* 4.3 6.3 - - + -
587D LEU* 1.3 85.7 - - - +
589D LEU* 1.3 66.9 + - - +
590D ALA* 3.6 19.1 - - + -
600D PRO* 4.7 11.8 - - + +
602D GLY* 4.1 7.2 - - - -
603D TYR 3.1 20.6 - - - +
604D ARG* 3.3 11.4 - - + +
605D ILE* 4.4 3.1 - - - +
708D TYR* 3.9 28.6 - + - -
709D ASN* 5.6 0.2 + - - -
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Residues in contact with LEU 589 (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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530D LEU* 4.4 25.6 - - + +
532D VAL* 3.7 15.1 - - + +
537D ASN* 4.4 8.1 - - + -
538D TRP 3.1 5.8 - - - +
539D VAL* 3.4 33.9 - - + -
587D LEU* 6.0 0.9 - - + -
588D TYR* 1.3 80.7 - - - +
590D ALA* 1.3 57.3 + - - +
602D GLY* 3.1 0.5 - - - -
603D TYR 2.7 34.2 + - - +
605D ILE* 4.7 13.5 - - + -
634D VAL* 4.2 16.2 - - + -
674D LEU* 4.2 25.4 - - + -
676D ALA* 4.7 14.1 - - + +
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Residues in contact with ALA 590 (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* 4.6 1.3 - - - -
537D ASN* 3.1 12.1 - - - -
538D TRP* 2.8 30.3 + - - -
540D TRP* 3.7 14.1 - - + +
588D TYR* 3.6 21.1 - - + -
589D LEU* 1.3 74.7 - - - +
591D SER* 1.3 66.3 + - - +
600D PRO* 4.2 5.8 - - + -
601D ARG 3.5 2.7 - - - +
602D GLY* 3.3 22.2 - - - +
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Residues in contact with SER 591 (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 4.3 - - - -
533D ALA* 3.6 28.2 + - - +
536D GLU 4.2 9.2 + - - -
537D ASN* 4.2 2.0 - - - +
538D TRP* 3.8 6.3 - - - -
540D TRP* 4.9 2.3 + - - -
590D ALA* 1.3 79.2 - - - +
592D ASN* 1.3 70.2 + - - +
593D HIS* 3.2 33.6 + - - -
600D PRO* 3.6 17.5 - - - +
601D ARG* 2.9 19.7 + - - -
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Residues in contact with ASN 592 (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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536D GLU* 4.3 3.5 + - + +
538D TRP* 3.1 34.0 - - + -
591D SER* 1.3 79.4 + - - +
593D HIS* 1.3 70.8 + - + +
594D SER* 4.1 2.1 + - - -
600D PRO* 5.1 3.3 - - - +
1L NAG 1.5 86.6 + - - +
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Residues in contact with HIS 593 (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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533D ALA* 4.5 11.2 - - + -
591D SER* 3.2 21.6 + - - +
592D ASN* 1.3 89.5 - - + +
594D SER* 1.3 63.8 + - - +
600D PRO* 3.5 4.1 - - - +
601D ARG* 3.1 33.5 + - - +
1L NAG 3.9 37.6 + - - +
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Residues in contact with SER 594 (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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592D ASN 4.1 2.3 + - - -
593D HIS* 1.3 77.6 - - - +
595D ASN* 1.3 62.2 + - - +
596D LYS 3.9 0.9 + - - -
598D GLY* 3.5 15.3 + - - -
599D HIS* 3.0 27.2 + - - -
600D PRO* 4.0 3.1 - - - +
601D ARG* 3.9 6.4 - - - +
1L NAG 5.5 1.8 - - - +
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Residues in contact with ASN 595 (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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688C ALA* 3.6 5.7 - - - +
594D SER* 1.3 73.5 - - - +
596D LYS* 1.3 50.6 + - - +
597D TRP* 2.5 25.8 + - - +
598D GLY* 2.4 34.8 + - - -
599D HIS* 2.6 33.3 + - - +
601D ARG* 3.6 12.9 - - + +
709D ASN* 3.0 25.5 + - - +
710D PHE 3.8 4.9 - - - +
711D PHE 3.0 22.2 + - - -
712D ASP* 3.3 15.5 + - - +
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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