Contacts of the strand formed by residues 600 - 608 (chain C) 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 PRO 600 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540C TRP* 4.5 20.4 - - + +
566C ARG* 4.0 19.9 + - - +
588C TYR* 5.3 3.8 - - + +
590C ALA* 4.0 14.3 - - + +
591C SER 4.0 16.2 - - - +
592C ASN 5.2 3.6 - - - +
593C HIS 3.8 6.7 - - - +
594C SER* 4.1 6.1 - - - +
598C GLY 4.3 3.4 - - - +
599C HIS* 1.3 87.8 - - + +
601C ARG* 1.3 63.7 + - - +
602C GLY* 3.3 3.6 + - - -
708C TYR* 3.8 2.8 - - - +
709C ASN* 3.4 15.6 + - - +
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Residues in contact with ARG 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C GLU* 3.2 34.2 + - - -
532C VAL* 3.0 8.7 - - + +
533C ALA* 3.5 16.6 - - - +
590C ALA* 4.2 0.7 - - - -
591C SER* 2.8 33.6 + - - +
593C HIS* 2.9 26.5 + - + +
594C SER 3.6 14.4 - - - -
595C ASN* 3.7 18.3 - - - +
600C PRO* 1.3 69.5 - - - +
602C GLY* 1.3 58.7 + - - +
709C ASN 3.3 8.7 - - - +
710C PHE* 2.5 53.9 + - + +
711C PHE* 4.7 3.4 - - - +
712C ASP* 5.5 2.6 + - - -
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Residues in contact with GLY 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C VAL* 4.0 3.4 - - - -
588C TYR* 4.4 4.9 - - - -
589C LEU 3.3 11.7 - - - -
590C ALA* 3.9 6.3 - - - -
600C PRO 3.3 2.2 + - - -
601C ARG* 1.3 75.7 - - - +
603C TYR* 1.3 65.9 + - - -
708C TYR* 2.8 41.2 + - - +
710C PHE* 3.3 12.1 - - - +
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Residues in contact with TYR 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C LEU* 3.2 36.9 - - + +
483C GLY* 2.3 36.9 + - - -
485C ILE* 5.0 1.8 - - + -
530C LEU* 4.2 25.0 - - + +
532C VAL* 4.6 7.1 - - + +
588C TYR* 2.7 23.2 - - - +
589C LEU* 2.9 19.9 + - - +
602C GLY* 1.3 80.8 - - - -
604C ARG* 1.3 55.9 + - - +
605C ILE* 4.8 3.6 - - - +
705C LEU* 3.2 40.2 - - + -
706C ARG 3.2 5.4 - - - -
707C PRO* 3.6 15.5 - - + +
710C PHE* 3.5 33.4 - + - -
711C PHE* 4.0 4.7 - - - -
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Residues in contact with ARG 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585C ARG 2.6 34.1 + - - -
586C TYR* 3.4 45.8 + - - +
587C LEU 3.2 10.5 + - - +
588C TYR* 3.0 17.5 - - + -
603C TYR* 1.3 75.4 - - - +
605C ILE* 1.3 62.6 + - - +
606C GLN* 4.7 29.3 - - - +
704C PHE 3.3 4.2 - - - +
705C LEU* 3.4 4.3 - - - +
706C ARG* 2.9 77.3 + - + +
707C PRO 5.4 0.4 - - - -
708C TYR* 4.4 10.6 - - + +
683D LEU 5.5 0.2 + - - -
687D HIS* 5.7 2.2 - - - -
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Residues in contact with ILE 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528C VAL* 5.6 2.0 - - + -
530C LEU* 5.0 6.3 - - + -
585C ARG 5.7 0.2 - - - +
587C LEU* 2.9 22.2 + - + +
588C TYR* 5.3 1.8 - - - -
589C LEU* 4.8 17.3 - - + -
603C TYR 4.8 4.7 - - - +
604C ARG* 1.3 75.6 + - - +
606C GLN* 1.3 62.5 + - - +
607C MET* 3.4 17.0 + - + +
632C LEU* 4.5 19.8 - - + +
634C VAL* 5.9 0.4 - - + -
676C ALA* 3.7 30.1 - - + -
678C VAL* 4.1 21.8 - - + -
703C PHE* 4.7 3.8 - - + -
704C PHE 3.5 6.3 - - - +
705C LEU* 3.7 21.1 - - + -
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Residues in contact with GLN 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C ARG* 3.7 25.1 + - - +
605C ILE* 1.3 72.5 - - - +
607C MET* 1.3 66.6 + - - +
608C LEU* 4.3 8.3 - - + -
703C PHE* 3.1 7.2 - - - +
704C PHE* 2.8 47.9 + - + +
706C ARG* 3.2 32.9 + - - +
610D PHE* 3.1 37.5 - - + -
698D GLY* 3.5 26.1 + - - +
699D ASN* 5.5 1.0 + - - +
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Residues in contact with MET 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583C THR* 6.0 3.4 - - - -
605C ILE* 3.4 14.8 + - + +
606C GLN* 1.3 79.3 - - - +
608C LEU* 1.3 68.1 + - - +
609C SER* 3.3 21.4 + - - +
631C GLN* 3.5 46.2 - - + +
632C LEU* 4.2 11.2 - - - -
678C VAL* 3.8 19.7 - - + -
679C THR 3.3 26.5 - - - +
702C GLY 5.5 0.4 - - - +
703C PHE* 4.1 2.7 - - + -
610D PHE* 4.4 10.6 - - - -
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Residues in contact with LEU 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C ARG* 3.6 30.5 - - + +
606C GLN* 4.3 10.3 - - + -
607C MET* 1.3 83.6 - - - +
609C SER* 1.3 63.0 + - - +
610C PHE* 5.0 4.3 - - + -
701C VAL* 3.3 11.4 - - + +
702C GLY 3.2 29.8 + - - +
703C PHE* 4.0 17.5 - - - +
704C PHE* 3.1 42.6 - - + -
610D PHE* 4.4 15.7 - - + -
698D GLY 5.9 0.4 - - - +
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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