Contacts of the helix formed by residues 591 - 603 (chain C) in PDB entry 1LQF
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 THR 591 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543C ARG* 4.3 12.0 + - - +
567C ILE* 5.2 8.5 - - + -
585C GLN* 4.6 9.9 - - + +
587C PRO* 3.7 12.6 - - + -
588C LEU* 2.7 43.0 + - + +
590C ASN* 1.3 86.8 + - - +
592C CYS* 1.3 60.4 + - - +
593C GLY 3.4 2.2 - - - -
594C HIS* 3.5 23.1 + - + +
595C PHE* 3.1 19.5 + - + +
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Residues in contact with CYS 592 (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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587C PRO* 4.2 4.7 - - - -
588C LEU 3.4 14.8 - - - -
589C PRO* 4.3 10.3 - - - +
590C ASN 3.6 1.0 - - - -
591C THR* 1.3 76.4 - - - +
593C GLY* 1.3 65.0 + - - +
595C PHE* 3.2 8.7 + - - +
596C TRP* 3.2 26.7 + - - -
622C ALA* 3.9 18.4 - - - -
623C GLN 4.9 2.5 - - - -
624C TYR* 3.7 27.4 - - + -
633C MET* 6.3 0.2 - - - -
635C PHE* 3.8 21.3 - - + -
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Residues in contact with GLY 593 (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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590C ASN 5.0 1.0 + - - -
591C THR 3.4 0.4 - - - -
592C CYS* 1.3 77.4 - - - +
594C HIS* 1.3 56.4 + - - +
596C TRP* 3.3 2.4 + - - +
597C GLU* 2.9 26.3 + - - +
635C PHE* 3.8 18.3 - - - -
637C ASP* 3.8 15.9 + - - -
638C THR* 3.2 28.5 + - - -
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Residues in contact with HIS 594 (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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543C ARG* 3.4 45.9 + - + -
559C LEU* 3.7 25.3 - - + +
561C GLN* 4.3 13.5 + - - -
566C TYR 4.6 1.4 + - - -
567C ILE* 3.9 12.9 - - + +
590C ASN* 3.8 16.5 + - - -
591C THR* 3.5 25.6 + - - +
592C CYS 3.2 0.2 - - - -
593C GLY* 1.3 75.4 - - - +
595C PHE* 1.3 57.4 + - - +
597C GLU* 3.2 9.8 + - - +
598C MET* 2.9 30.7 + - - +
637C ASP* 4.2 17.4 + - + +
638C THR* 4.4 2.5 - - + -
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Residues in contact with PHE 595 (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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567C ILE* 4.0 11.4 - - + +
584C THR* 4.0 15.5 - - + -
587C PRO* 3.5 26.2 - - + -
591C THR* 3.1 11.6 + - + +
592C CYS* 3.3 9.2 - - - +
593C GLY 3.2 0.2 - - - -
594C HIS* 1.3 80.3 - - - +
596C TRP* 1.3 86.2 + + - +
598C MET* 3.4 13.7 + - + +
599C VAL* 3.1 36.8 + - + +
607C VAL* 3.8 25.8 - - + -
624C TYR* 3.5 29.4 - + - -
712C VAL* 3.8 23.3 - - + -
714C HIS* 4.2 6.5 - + - -
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Residues in contact with TRP 596 (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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592C CYS 3.2 21.7 + - - +
593C GLY 4.0 2.0 - - - +
595C PHE* 1.3 87.6 - + - +
597C GLU* 1.3 65.7 + - - +
599C VAL* 3.3 33.7 + - + +
600C TRP* 2.9 23.7 + - - +
607C VAL* 4.4 9.0 - - + -
624C TYR* 2.8 48.4 + + + +
625C TRP* 4.7 1.3 - - + -
635C PHE* 3.4 28.3 - + + -
640C LEU* 3.5 16.4 - - + +
642C LEU* 3.5 26.2 - - + +
658C LEU* 4.1 22.7 - - + -
660C LEU* 4.1 22.6 - - + +
671C ILE* 4.2 13.2 - - + -
673C HIS* 5.2 0.7 - + - -
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Residues in contact with GLU 597 (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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559C LEU* 3.7 15.4 - - + +
560C HIS 3.7 6.4 + - - +
561C GLN* 2.9 43.0 + - - +
593C GLY 2.9 16.7 + - - +
594C HIS* 3.2 3.7 + - - +
596C TRP* 1.3 77.9 - - - +
598C MET* 1.3 53.8 + - - +
600C TRP* 3.3 2.8 + - - +
601C GLU* 2.5 72.1 + - + +
638C THR* 3.3 21.0 - - + +
640C LEU* 3.4 10.4 - - + +
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Residues in contact with MET 598 (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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557C ILE* 3.8 24.0 - - + -
559C LEU* 4.0 13.9 - - + -
567C ILE* 4.2 18.4 - - + -
569C ALA* 4.0 14.6 - - + -
582C ILE* 3.9 26.5 - - + -
584C THR* 4.5 3.6 - - + -
594C HIS 2.9 15.2 + - - +
595C PHE* 3.5 24.9 - - + +
597C GLU* 1.3 75.1 - - - +
599C VAL* 1.3 59.9 + - - +
601C GLU* 4.6 3.4 - - - -
602C GLN* 2.8 51.2 + - + +
712C VAL* 4.3 18.4 - - + -
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Residues in contact with VAL 599 (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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595C PHE* 3.1 27.1 + - + +
596C TRP* 3.5 35.4 - - + +
597C GLU 3.3 0.2 - - - -
598C MET* 1.3 77.8 - - + +
600C TRP* 1.3 63.8 + - - +
603C LYS* 3.0 17.3 + - - -
604C SER* 3.2 28.1 + - - +
607C VAL* 4.4 4.5 - - + -
660C LEU* 4.1 3.4 - - + -
669C ARG* 4.5 0.3 + - - -
671C ILE* 3.7 32.1 - - + -
712C VAL* 4.2 18.6 - - + -
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Residues in contact with TRP 600 (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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562A GLU* 3.2 31.6 + - - -
596C TRP 2.9 17.1 + - - +
597C GLU* 3.6 5.4 - - - +
599C VAL* 1.3 78.4 - - - +
601C GLU* 1.3 73.3 + - + +
603C LYS* 3.0 8.5 + - - +
640C LEU* 4.2 18.8 - - + -
660C LEU* 3.5 44.2 - - + -
662C ASN* 3.4 26.7 - - + +
667C GLU* 3.1 57.2 - - + -
669C ARG* 2.7 53.8 + - + +
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Residues in contact with GLU 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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562A GLU* 6.0 0.2 - - - +
558C LYS 4.4 1.0 - - - +
559C LEU* 3.5 10.0 - - - +
560C HIS* 2.8 67.0 + - + +
597C GLU* 2.5 59.9 + - + +
598C MET* 4.0 3.2 - - - +
600C TRP* 1.3 82.5 - - + +
602C GLN* 1.3 67.5 + - - +
603C LYS* 3.5 12.7 + - - +
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Residues in contact with GLN 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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558A LYS* 6.0 0.5 + - - -
557C ILE* 3.9 26.6 - - + +
558C LYS 4.1 11.9 + - - -
560C HIS* 4.3 11.7 + - - -
582C ILE* 3.9 17.0 - - + +
598C MET* 2.8 35.0 + - + +
601C GLU* 1.3 85.3 + - - +
603C LYS* 1.3 72.2 + - - +
604C SER* 3.9 12.6 - - - +
709C GLY* 3.3 14.6 - - - -
710C PRO* 4.1 7.6 - - + +
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Residues in contact with LYS 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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558A LYS* 6.3 1.6 - - - -
561A GLN 5.8 2.0 + - - -
562A GLU* 5.2 6.3 + - - -
565A ASP* 4.7 13.7 - - - -
599C VAL 3.0 2.5 + - - -
600C TRP* 3.0 15.6 + - - +
601C GLU* 4.0 10.9 + - - +
602C GLN* 1.3 82.6 - - - +
604C SER* 1.3 56.8 + - - +
605C ARG* 2.4 44.5 + - - +
669C ARG* 3.5 24.5 - - - +
709C GLY* 2.8 21.0 + - - +
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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