Contacts of the helix formed by residues 591 - 603 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543A ARG* 4.2 23.4 + - - +
567A ILE* 5.2 9.3 - - + +
585A GLN* 4.6 9.6 - - - +
587A PRO* 3.7 13.5 - - + -
588A LEU* 2.8 34.3 + - + +
590A ASN* 1.3 81.3 + - - +
592A CYS* 1.3 63.4 + - - +
593A GLY 3.3 2.7 - - - -
594A HIS* 3.3 23.8 + - + +
595A PHE* 3.1 19.6 + - + +
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Residues in contact with CYS 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587A PRO* 4.2 4.9 - - - -
588A LEU 3.3 15.7 - - - -
589A PRO* 4.3 10.8 - - - +
590A ASN 3.5 1.4 - - - -
591A THR* 1.3 74.9 - - - +
593A GLY* 1.3 65.1 + - - +
595A PHE* 3.3 9.2 + - - +
596A TRP* 3.3 26.7 + - - -
622A ALA* 3.9 16.6 - - - -
623A GLN 4.8 2.5 - - - -
624A TYR* 3.7 28.9 - - + -
635A PHE* 3.8 21.8 - - + -
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Residues in contact with GLY 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A ASN 4.9 1.0 + - - -
591A THR 3.3 0.6 - - - -
592A CYS* 1.3 77.9 - - - +
594A HIS* 1.3 57.7 + - - +
596A TRP* 3.3 2.3 + - - +
597A GLU* 2.9 24.8 + - - +
635A PHE* 3.8 14.3 - - - -
637A ASP* 3.7 21.0 + - - -
638A THR* 3.2 28.8 + - - -
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Residues in contact with HIS 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A ARG* 3.3 48.2 + - + +
559A LEU* 3.8 27.1 - - + +
561A GLN* 4.3 11.7 + - - -
566A TYR 4.5 2.6 + - - -
567A ILE* 3.9 12.9 - - + +
590A ASN* 3.9 17.4 + - - -
591A THR* 3.4 25.4 + - - +
593A GLY* 1.3 78.1 - - - +
595A PHE* 1.3 56.4 + - - +
597A GLU* 3.1 8.4 + - - +
598A MET* 2.8 30.8 + - - +
637A ASP* 4.3 14.1 + - - +
638A THR* 4.5 2.5 - - + -
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Residues in contact with PHE 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A ILE* 3.9 11.6 - - + +
584A THR* 4.0 15.3 - - + -
587A PRO* 3.4 27.8 - - + -
591A THR* 3.1 11.1 + - + +
592A CYS* 3.4 9.9 - - - +
594A HIS* 1.3 78.6 - - - +
596A TRP* 1.3 91.8 + + - +
598A MET* 3.3 13.9 + - + +
599A VAL* 3.1 33.3 + - + +
607A VAL* 3.8 26.2 - - + -
624A TYR* 3.5 29.4 - + - -
712A VAL* 3.9 22.0 - - + -
714A HIS* 4.2 5.6 - + - -
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Residues in contact with TRP 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A CYS 3.3 16.7 + - - +
593A GLY 4.0 3.8 - - - +
595A PHE* 1.3 87.4 - + - +
597A GLU* 1.3 62.6 - - - +
598A MET 3.2 0.2 - - - -
599A VAL* 3.4 28.7 + - + +
600A TRP* 3.0 19.1 + - - +
607A VAL* 4.4 9.9 - - + -
624A TYR* 2.8 48.1 + + + +
625A TRP* 4.7 1.3 - - + -
635A PHE* 3.5 31.9 - + + -
640A LEU* 3.4 21.3 - - + +
642A LEU* 3.4 26.9 - - + +
658A LEU* 4.1 23.1 - - + -
660A LEU* 4.1 22.1 - - + +
671A ILE* 4.1 20.2 - - + -
673A HIS* 5.1 1.1 - + - -
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Residues in contact with GLU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A LEU* 3.9 14.8 - - + +
560A HIS 3.6 11.1 + - - +
561A GLN* 2.9 37.5 + - - +
593A GLY 2.9 14.1 + - - +
594A HIS* 3.1 7.4 + - - +
596A TRP* 1.3 77.1 - - - +
598A MET* 1.3 55.5 + - - +
600A TRP* 3.3 2.6 + - - +
601A GLU* 2.5 74.8 + - + +
638A THR* 3.4 20.7 - - + +
640A LEU* 3.5 9.6 - - + +
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Residues in contact with MET 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ILE* 3.9 20.2 - - + -
559A LEU* 4.0 14.1 - - + +
567A ILE* 4.2 17.7 - - + -
569A ALA* 3.9 15.0 - - + -
582A ILE* 3.9 32.5 - - + -
584A THR* 4.4 3.6 - - + -
594A HIS 2.8 11.5 + - - +
595A PHE* 3.4 22.4 - - + +
597A GLU* 1.3 76.4 - - - +
599A VAL* 1.3 60.2 + - + +
601A GLU* 4.7 4.5 - - - -
602A GLN* 2.8 51.1 + - + +
712A VAL* 4.3 21.8 - - + -
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Residues in contact with VAL 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A PHE* 3.1 27.6 + - + +
596A TRP* 3.5 31.6 - - + +
597A GLU 3.3 0.4 - - - -
598A MET* 1.3 74.7 - - - +
600A TRP* 1.3 59.6 + - - +
603A LYS* 3.0 24.1 + - - -
604A SER* 3.2 26.9 + - - +
607A VAL* 4.4 4.7 - - + -
660A LEU* 4.1 8.3 - - + -
669A ARG* 4.4 0.3 + - - -
671A ILE* 3.7 32.1 - - + -
712A VAL* 4.2 18.4 - - + -
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Residues in contact with TRP 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A TRP 3.0 17.8 + - - +
597A GLU* 3.6 4.7 - - - +
599A VAL* 1.3 79.4 - - - +
601A GLU* 1.3 68.1 + - + +
603A LYS* 3.3 5.7 + - - +
640A LEU* 4.2 18.8 - - + -
660A LEU* 3.6 36.8 - - + -
662A ASN* 3.6 21.7 - - + +
667A GLU* 3.1 63.7 - - + -
669A ARG* 2.7 55.2 + - + +
562C GLU* 2.4 42.9 + - - -
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Residues in contact with GLU 601 (chain A).
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 4.3 1.2 - - - +
559A LEU* 3.6 10.2 - - - +
560A HIS* 2.8 67.0 + - + +
597A GLU* 2.5 59.2 + - + +
598A MET* 4.1 2.9 - - - +
600A TRP* 1.3 83.9 - - + +
602A GLN* 1.3 68.7 + - - +
603A LYS* 3.6 13.4 + - - +
562C GLU* 4.9 4.9 - - - +
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Residues in contact with GLN 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ILE* 4.0 25.6 - - + +
558A LYS 4.1 12.5 + - - +
560A HIS* 4.2 12.3 + - - -
582A ILE* 3.9 23.2 - - + +
598A MET* 2.8 33.9 + - + +
601A GLU* 1.3 82.9 + - - +
603A LYS* 1.3 71.1 + - - +
604A SER* 3.3 12.3 - - - +
709A GLY* 3.3 15.2 - - - -
710A PRO* 4.1 8.0 - - + +
558C LYS* 5.5 4.5 + - - -
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Residues in contact with LYS 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A VAL 3.0 7.9 + - - -
600A TRP 3.3 7.4 + - - +
601A GLU* 4.0 9.1 + - - +
602A GLN* 1.3 82.7 - - - +
604A SER* 1.3 66.4 + - - +
605A ARG 3.8 0.5 + - - -
669A ARG* 3.4 40.1 - - - +
708A HIS* 4.3 5.9 + - - +
709A GLY* 2.8 22.3 + - - +
561C GLN 4.8 8.1 + - - -
562C GLU* 4.3 16.6 + - - -
565C ASP* 4.2 20.6 - - - -
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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