Contacts of the helix formed by residues 591 - 603 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543D ARG* 4.0 24.6 + - - +
567D ILE* 5.2 8.8 - - + +
585D GLN* 4.6 10.1 - - + +
587D PRO* 3.7 13.7 - - + -
588D LEU* 2.8 36.5 + - + +
590D ASN* 1.3 81.9 + - - +
592D CYS* 1.3 60.3 + - - +
593D GLY 3.4 2.9 - - - -
594D HIS* 3.3 23.6 + - + +
595D PHE* 3.1 19.0 + - + +
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Residues in contact with CYS 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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587D PRO* 4.1 4.5 - - - -
588D LEU 3.1 19.5 + - - -
589D PRO* 4.4 9.6 - - - +
590D ASN 3.6 1.4 - - - -
591D THR* 1.3 76.0 - - - +
593D GLY* 1.3 66.2 + - - +
595D PHE* 3.4 9.0 + - - +
596D TRP* 3.3 27.4 + - - -
622D ALA* 3.8 17.9 - - - -
623D GLN 4.7 2.9 - - - -
624D TYR* 3.6 29.4 - - + -
633D MET* 6.5 0.2 - - - -
635D PHE* 3.9 19.7 - - + -
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Residues in contact with GLY 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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590D ASN 4.9 1.2 + - - -
591D THR 3.4 0.6 - - - -
592D CYS* 1.3 77.9 - - - +
594D HIS* 1.3 56.3 + - - +
596D TRP* 3.4 3.1 + - - +
597D GLU 2.9 23.9 + - - -
635D PHE* 3.8 13.4 - - - -
637D ASP* 3.8 20.6 + - - -
638D THR* 3.3 29.8 + - - +
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Residues in contact with HIS 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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543D ARG* 2.9 43.4 + - + -
559D LEU* 3.8 25.2 - - + +
561D GLN* 5.2 8.5 + - - -
566D TYR 4.6 1.8 + - - -
567D ILE* 3.8 12.9 - - + +
590D ASN* 3.9 17.7 + - - -
591D THR* 3.4 25.1 + - - +
593D GLY* 1.3 77.9 - - - +
595D PHE* 1.3 55.6 + - - +
597D GLU* 3.1 9.6 + - - +
598D MET* 2.9 30.5 + - - +
637D ASP* 4.3 14.3 + - + +
638D THR* 4.5 8.3 - - + -
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Residues in contact with PHE 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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567D ILE* 3.9 11.4 - - + +
584D THR* 4.1 14.6 - - + -
587D PRO* 3.6 27.4 - - + -
591D THR* 3.1 10.8 + - + +
592D CYS* 3.4 10.1 - - - +
594D HIS* 1.3 78.5 - - - +
596D TRP* 1.3 88.9 + + - +
598D MET* 3.2 15.0 + - + +
599D VAL* 3.1 35.3 + - + +
607D VAL* 3.7 26.7 - - + -
624D TYR* 3.5 29.8 - + - -
712D VAL* 3.9 22.0 - - + -
714D HIS* 4.2 5.4 - + - -
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Residues in contact with TRP 596 (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 CYS 3.3 20.3 + - - +
593D GLY 4.0 3.4 - - - +
595D PHE* 1.3 89.3 - + - +
597D GLU* 1.3 63.8 + - - +
598D MET 3.2 0.2 - - - -
599D VAL* 3.4 34.3 + - + +
600D TRP* 3.0 19.8 + - - +
607D VAL* 4.4 9.2 - - + -
624D TYR* 2.8 46.3 + + + -
625D TRP* 4.7 1.1 - - + -
635D PHE* 3.5 27.1 - + + -
640D LEU* 3.4 22.1 - - + +
642D LEU* 3.4 27.0 - - + +
658D LEU* 4.1 22.9 - - + -
660D LEU* 4.1 20.4 - - + +
671D ILE* 4.2 15.5 - - + -
673D HIS* 5.1 1.1 - + - -
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Residues in contact with GLU 597 (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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559D LEU* 3.9 21.6 - - + +
560D HIS 3.1 20.4 + - - +
561D GLN* 3.6 14.6 - - - +
593D GLY 2.9 17.6 + - - +
594D HIS* 3.1 4.6 + - - +
596D TRP* 1.3 73.7 - - - +
598D MET* 1.3 57.6 + - - +
600D TRP* 3.3 2.4 + - - +
601D GLU* 2.5 75.2 + - + +
638D THR* 3.3 29.3 - - + +
640D LEU* 3.4 8.7 - - + +
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Residues in contact with MET 598 (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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557D ILE* 3.8 31.9 - - + -
559D LEU* 4.0 14.1 - - + +
567D ILE* 4.2 19.1 - - + -
569D ALA* 3.9 15.7 - - + -
582D ILE* 3.8 28.5 - - + -
584D THR* 4.4 4.0 - - + -
594D HIS 2.9 12.4 + - - +
595D PHE* 3.4 21.1 - - + +
597D GLU* 1.3 75.7 - - - +
599D VAL* 1.3 60.8 + - + +
601D GLU* 4.6 3.1 - - - -
602D GLN* 2.8 45.2 + - + +
712D VAL* 4.3 22.2 - - + -
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Residues in contact with VAL 599 (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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595D PHE* 3.1 24.2 + - + +
596D TRP* 3.6 32.1 - - + +
598D MET* 1.3 78.8 - - + +
600D TRP* 1.3 56.7 + - - +
603D LYS* 3.0 23.6 + - - -
604D SER* 3.2 28.4 + - - +
607D VAL* 4.4 4.7 - - + -
660D LEU* 4.1 8.3 - - + -
669D ARG* 4.3 0.3 + - - -
671D ILE* 3.7 32.1 - - + -
712D VAL* 4.2 19.7 - - + -
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Residues in contact with TRP 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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596D TRP 3.0 16.7 + - - +
597D GLU* 3.6 5.4 - - - +
599D VAL* 1.3 78.9 - - - +
601D GLU* 1.3 71.4 + - + +
603D LYS* 3.3 8.7 + - - +
640D LEU* 4.2 20.2 - - + -
660D LEU* 3.6 38.3 - - + +
662D ASN* 3.6 31.4 - - + +
667D GLU* 3.0 64.8 + - + -
669D ARG* 2.8 58.1 + - + +
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Residues in contact with GLU 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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558D LYS 4.3 0.7 - - - +
559D LEU* 3.6 9.9 - - - +
560D HIS* 2.8 66.0 + - + +
597D GLU* 2.5 58.3 + - + +
598D MET* 4.1 2.9 - - - +
600D TRP* 1.3 83.6 - - + +
602D GLN* 1.3 68.0 + - - +
603D LYS* 3.6 13.8 + - - +
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Residues in contact with GLN 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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557D ILE* 4.1 24.4 - - + +
558D LYS 4.2 7.5 + - - +
560D HIS* 4.0 20.8 + - - -
582D ILE* 3.9 23.4 - - + +
598D MET* 2.8 28.9 + - + +
601D GLU* 1.3 81.0 + - - +
603D LYS* 1.3 73.1 + - - +
604D SER* 3.4 11.9 - - - +
709D GLY* 3.2 15.1 - - - -
710D PRO* 4.1 7.7 - - + +
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Residues in contact with LYS 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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599D VAL 3.0 7.9 + - - -
600D TRP* 3.3 11.1 + - - +
601D GLU* 3.9 10.8 + - - +
602D GLN* 1.3 82.7 - - - +
604D SER* 1.3 64.9 + - - +
605D ARG* 3.9 2.6 + - - +
669D ARG* 3.4 37.9 - - - +
708D HIS* 4.2 6.3 + - - +
709D GLY* 2.8 22.7 + - - +
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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