Contacts of the helix formed by residues 629 - 645 (chain D) in PDB entry 1HQR
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 PHE 629 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628D THR* 1.3 72.5 - - - +
630D GLN* 1.3 53.1 + - - +
632D ILE* 3.8 9.4 - - + +
633D ASP* 2.5 39.7 + - - +
660D ILE* 3.6 45.1 - - + -
668D GLU* 3.5 31.4 - - + -
670D ILE* 3.9 18.1 - - + +
688D TYR* 4.9 3.4 - - + -
692D ARG* 3.0 53.2 + - + +
693D ILE 3.4 23.8 - - - -
694D ILE* 4.1 14.1 - - + -
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Residues in contact with GLN 630 (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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572D PHE* 3.9 6.3 - - + +
573D GLY* 3.0 13.0 - - - -
574D LEU* 2.6 49.5 + - + +
587D TYR 2.8 25.8 + - - +
589D GLY* 3.6 9.0 + - - +
628D THR* 2.9 10.9 - - - +
629D PHE* 1.3 80.5 - - - +
631D GLU* 1.3 56.2 + - - +
633D ASP* 3.4 0.9 - - - +
634D PHE* 2.7 35.5 + - + +
688D TYR* 3.4 52.8 + - + +
692D ARG 4.7 0.8 + - - -
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Residues in contact with GLU 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D PHE* 3.1 42.0 - - + +
591D THR* 5.7 0.3 - - - +
622D LEU* 4.5 8.0 - - + +
623D GLU 5.1 2.8 + - - -
624D LYS* 2.9 41.0 + - - +
627D VAL* 3.1 24.8 - - + +
628D THR* 3.0 17.2 + - - +
630D GLN* 1.3 81.5 - - - +
632D ILE* 1.3 63.4 + - - +
634D PHE* 3.6 0.7 + - - +
635D LYS* 3.4 44.5 + - - +
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Residues in contact with ILE 632 (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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602D LEU* 4.8 5.8 - - + -
622D LEU* 3.9 31.4 - - + -
627D VAL* 4.5 5.4 - - + -
628D THR 3.0 14.4 + - - +
629D PHE* 3.8 10.3 - - + +
631D GLU* 1.3 78.0 - - - +
633D ASP* 1.3 65.9 + - - +
634D PHE 3.3 0.3 + - - -
635D LYS* 3.5 2.6 + - - +
636D ILE* 3.3 35.2 + - + +
660D ILE* 3.7 28.3 - - + -
670D ILE* 6.1 0.4 - - + -
694D ILE* 4.0 19.5 - - + -
696D MET* 4.6 0.4 - - - -
699D PHE* 3.4 35.2 - - + -
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Residues in contact with ASP 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517D TYR* 4.2 0.3 - - - -
629D PHE 2.5 23.4 + - - +
630D GLN* 3.4 2.7 - - - +
632D ILE* 1.3 75.9 - - - +
634D PHE* 1.3 63.5 + - - +
636D ILE* 4.1 1.4 - - - +
637D ARG* 2.8 54.7 + - - +
658D ILE* 3.8 15.7 - - - +
670D ILE* 3.2 36.3 - - + +
687D LYS* 5.0 0.2 - - - -
688D TYR* 2.6 30.2 + - + +
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Residues in contact with PHE 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517D TYR* 4.1 19.3 - + + -
519D ILE* 3.7 29.4 - - + -
521D PRO* 4.0 19.5 - - + -
572D PHE* 4.3 17.5 - + + -
574D LEU* 3.4 44.4 - - + -
630D GLN* 2.7 19.1 + - + +
631D GLU 3.9 4.0 - - - +
633D ASP* 1.3 75.5 + - - +
635D LYS* 1.3 70.9 + - + +
637D ARG* 3.0 8.3 + - - +
638D LYS* 2.8 59.7 + - + +
641D MET* 5.4 0.9 - - + -
688D TYR* 4.7 0.2 + - - -
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Residues in contact with LYS 635 (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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572D PHE* 4.1 17.8 - - + -
620D ILE* 4.3 21.8 - - + +
621D ILE 3.7 18.4 + - - +
622D LEU* 4.2 18.8 - - + +
623D GLU* 5.1 3.4 - - - +
631D GLU* 3.4 38.4 + - - +
632D ILE* 4.1 2.2 - - - +
634D PHE* 1.3 88.4 - - + +
636D ILE* 1.3 58.5 + - - +
638D LYS* 3.2 5.8 + - + +
639D TYR* 2.8 31.0 + - - +
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Residues in contact with ILE 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602D LEU* 5.2 2.5 - - + -
620D ILE* 3.6 24.7 - - + +
632D ILE* 3.3 35.1 + - + +
633D ASP 4.1 0.2 - - - +
635D LYS* 1.3 77.4 - - + +
637D ARG* 1.3 57.5 + - - +
639D TYR* 3.3 3.3 + - + +
640D LEU* 2.9 29.8 + - + +
658D ILE* 3.4 39.9 - - + -
702D PHE* 4.0 34.5 - - + -
704D ILE* 3.8 25.6 - - + -
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Residues in contact with ARG 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513D LEU* 4.4 4.0 - - - +
517D TYR* 3.5 48.0 + - + -
633D ASP* 2.8 43.4 + - - +
634D PHE* 3.0 8.6 + - - +
636D ILE* 1.3 77.5 - - - +
638D LYS* 1.3 55.2 + - - +
640D LEU* 3.1 7.9 + - - +
641D MET* 2.7 50.0 + - + +
646D ILE* 5.1 0.4 - - + -
647D TYR* 2.5 36.3 + - + +
658D ILE* 4.7 0.4 - - + -
670D ILE* 4.0 5.5 - - - +
671D ASP 3.3 21.1 + - - -
672D LEU* 3.2 32.0 + - + -
687D LYS* 4.1 10.1 - - - +
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Residues in contact with LYS 638 (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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634D PHE* 2.8 46.3 + - + +
635D LYS* 3.2 8.9 + - + +
637D ARG* 1.3 72.0 - - - +
639D TYR* 1.3 60.2 + - - +
641D MET* 3.2 15.9 + - + +
642D ASP* 2.4 70.7 + - - +
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Residues in contact with TYR 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616D LEU* 3.0 51.7 - - + +
619D LYS* 4.6 23.0 - - + +
620D ILE* 4.4 16.2 - - + -
635D LYS 2.8 17.2 + - - +
636D ILE* 3.5 7.0 - - + +
638D LYS* 1.3 79.1 - - - +
640D LEU* 1.3 77.6 + - + +
642D ASP* 3.2 3.1 + - - -
643D ASN* 2.8 59.2 + - - +
644D TYR* 4.1 13.0 - + - -
702D PHE* 6.5 0.2 - + - -
704D ILE* 5.5 1.1 - - + -
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Residues in contact with LEU 640 (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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606D LEU* 4.7 4.3 - - + -
616D LEU* 4.7 2.9 - - + -
636D ILE* 2.9 25.1 + - + +
637D ARG* 3.4 4.7 - - - +
639D TYR* 1.3 87.8 - - + +
641D MET* 1.3 57.8 + - - +
644D TYR* 2.7 49.7 + - + +
645D LYS 3.1 4.7 + - - -
646D ILE* 3.6 26.6 - - + +
672D LEU* 3.8 30.3 - - + -
704D ILE* 3.6 40.8 - - + -
706D LEU* 4.7 3.1 - - + -
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Residues in contact with MET 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514D LEU* 4.8 8.7 - - - +
517D TYR* 3.4 44.2 - - + +
518D THR* 5.2 3.8 - - - -
634D PHE* 5.4 1.6 - - + -
637D ARG* 2.7 25.6 + - + +
638D LYS* 3.4 29.6 - - + +
640D LEU* 1.3 72.3 - - - +
642D ASP* 1.3 63.3 + - - +
643D ASN 2.8 3.1 + - - -
645D LYS* 2.8 40.8 + - - +
646D ILE* 4.1 18.2 - - + +
647D TYR* 3.6 26.5 - - + -
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Residues in contact with ASP 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638D LYS* 2.4 58.1 + - - +
639D TYR* 3.6 6.2 - - - +
641D MET* 1.3 74.4 - - - +
643D ASN* 1.3 69.3 + - - +
645D LYS* 3.7 21.9 + - - +
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Residues in contact with ASN 643 (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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639D TYR* 2.8 54.7 + - + +
641D MET 2.8 3.8 + - - -
642D ASP* 1.3 88.4 - - - +
644D TYR* 1.3 80.0 + - + +
645D LYS* 3.5 7.5 - - - +
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Residues in contact with TYR 644 (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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606D LEU* 3.1 25.8 - - + +
608D ILE* 4.0 15.5 - - + -
611D GLU* 6.1 0.2 - - - -
614D GLN* 3.0 33.4 + - - -
616D LEU* 4.1 3.8 - - - +
639D TYR* 4.1 20.9 - + - -
640D LEU* 2.7 29.6 + - + +
643D ASN* 1.3 87.8 - - + +
645D LYS* 1.3 72.9 + - - +
646D ILE* 3.0 15.2 + - + -
651D SER* 4.8 0.7 - - - -
652D PRO* 5.8 0.2 - - - +
653D TYR* 3.6 34.9 + + + +
706D LEU* 4.8 2.2 - - + -
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Residues in contact with LYS 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640D LEU 3.1 0.2 + - - -
641D MET* 2.8 24.7 + - - +
642D ASP* 3.7 26.8 + - - +
643D ASN* 4.6 5.6 - - - +
644D TYR* 1.3 79.5 - - - +
646D ILE* 1.3 56.2 + - - +
647D TYR 2.9 12.5 + - - -
648D ASP* 3.1 33.5 + - + +
651D SER* 3.0 20.5 - - - -
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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
------------------------------------------------------------
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