Contacts of the helix formed by residues 638 - 656 (chain D) in PDB entry 1M2Z
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 CYS 638 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556D THR* 3.8 14.9 + - + -
560D MET* 5.4 2.0 - - + -
636D LEU 2.8 1.0 + - - -
637D PRO* 1.3 92.3 - - - +
639D MET* 1.3 58.6 + - - +
641D ASP* 2.8 28.7 - - - +
642D GLN* 2.7 31.4 + - - +
735D TYR* 3.8 16.2 + - - +
745D MET* 6.6 0.2 - - - -
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Residues in contact with MET 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D DEX 5.8 0.9 - - - +
556D THR* 4.4 6.6 + - + -
559D ILE* 4.3 17.5 - - + -
560D MET* 4.3 16.2 - - + -
563D LEU* 5.6 3.6 - - + -
629D ILE* 3.6 20.9 - - + -
633D ARG* 3.2 29.6 - - - +
634D MET* 3.5 17.0 - - - +
636D LEU* 3.2 18.9 + - + +
638D CYS* 1.3 77.0 - - - +
640D TYR* 1.3 59.9 + - - +
642D GLN* 3.1 27.9 - - + +
643D CYS* 3.0 51.1 + - - -
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Residues in contact with TYR 640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634D MET* 3.5 39.1 + - + +
636D LEU 4.7 1.2 + - - -
638D CYS 3.5 0.6 - - - -
639D MET* 1.3 74.2 - - - +
641D ASP* 1.3 70.3 + - - +
642D GLN 2.9 3.7 + - - -
643D CYS 4.3 0.4 - - - +
644D LYS* 3.0 59.5 + - + +
647D LEU* 4.0 21.8 - - + +
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Residues in contact with ASP 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636D LEU 5.2 0.3 - - - +
637D PRO 4.3 3.6 - - - +
638D CYS* 2.8 32.6 - - - +
640D TYR* 1.3 77.6 + - - +
642D GLN* 1.3 57.8 + - - +
644D LYS* 3.5 25.9 - - - +
645D HIS* 4.2 9.0 + - - -
735D TYR* 3.7 27.8 - - + +
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Residues in contact with GLN 642 (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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401D DEX 3.1 36.7 + - + +
560D MET* 3.0 39.2 - - - +
638D CYS* 2.7 29.9 + - - +
639D MET* 3.1 32.3 - - + +
641D ASP* 1.3 77.8 - - - +
643D CYS* 1.3 63.8 + - - +
644D LYS 3.3 2.1 + - - -
645D HIS* 3.8 7.9 + - - -
646D MET* 3.3 13.6 - - + +
732D LEU* 3.7 14.5 - - - +
735D TYR* 3.7 23.1 - - + -
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Residues in contact with CYS 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D LEU* 3.6 15.9 - - + -
623D PHE* 4.7 0.9 - - - -
629D ILE* 3.5 31.2 - - - -
634D MET* 3.9 17.5 - - + -
639D MET* 3.0 40.9 + - - +
642D GLN* 1.3 75.8 - - - +
644D LYS* 1.3 60.2 + - - +
645D HIS 3.1 2.9 - - - -
646D MET* 2.9 18.1 + - - +
647D LEU* 2.8 31.2 + - - +
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Residues in contact with LYS 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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640D TYR* 3.0 48.5 + - + +
641D ASP* 3.5 23.9 - - - +
642D GLN 3.3 0.4 - - - -
643D CYS* 1.3 77.3 - - - +
645D HIS* 1.3 89.5 - - + +
647D LEU* 3.5 15.0 - - - +
648D TYR* 3.0 23.0 + - - +
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Residues in contact with HIS 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641D ASP 4.2 11.9 + - - -
642D GLN* 3.8 4.9 + - - -
643D CYS 3.1 0.8 - - - -
644D LYS* 1.3 101.6 - - + +
646D MET* 1.3 65.0 - - - +
647D LEU 3.2 0.2 - - - -
648D TYR* 3.1 25.1 + + + +
649D VAL* 3.2 11.7 - - - +
728D VAL* 4.4 15.8 - - + +
731D ASN* 3.6 45.4 + - + +
732D LEU* 4.0 21.9 - - + +
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Residues in contact with MET 646 (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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401D DEX 3.6 46.0 - - + +
605D ALA* 5.2 3.3 - - + +
608D LEU* 3.5 30.7 - - + -
609D GLY* 4.6 2.9 + - - -
621D LEU* 3.7 15.3 - - + +
623D PHE* 3.6 21.3 - - + -
642D GLN* 3.3 26.9 - - + +
643D CYS* 2.9 15.5 + - - +
645D HIS* 1.3 76.4 - - - +
647D LEU* 1.3 64.5 + - - +
649D VAL* 3.2 22.0 - - - +
650D SER* 3.3 11.1 + - - -
732D LEU* 4.1 18.4 - - + -
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Residues in contact with LEU 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D ALA 4.0 21.5 - - - +
619D ASN 4.1 16.4 - - - +
620D LEU 4.9 0.2 - - - -
621D LEU* 3.8 26.5 - - + +
634D MET* 3.8 23.3 - - + -
640D TYR* 4.0 24.5 - - + +
643D CYS 2.8 15.5 + - - +
644D LYS* 3.5 9.2 - - - +
646D MET* 1.3 75.3 - - - +
648D TYR* 1.3 53.8 + - - +
650D SER* 3.2 3.7 + - - -
651D SER* 2.8 36.7 + - - -
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Residues in contact with TYR 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644D LYS 3.0 14.2 + - - +
645D HIS* 3.1 18.4 - + + +
647D LEU* 1.3 75.2 - - - +
649D VAL* 1.3 67.9 + - + +
651D SER* 3.1 9.5 + - - -
652D GLU* 3.0 55.6 + - + +
721D LEU* 5.0 3.1 - - + +
724D SER* 3.5 31.7 + - - -
728D VAL* 4.2 22.7 - - + -
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Residues in contact with VAL 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605D ALA* 3.7 15.0 - - + +
606D PHE* 4.3 15.5 - - + -
609D GLY* 3.6 20.9 - - - -
645D HIS 3.2 17.9 - - - +
646D MET* 3.2 13.0 - - - +
648D TYR* 1.3 82.9 - - + +
650D SER* 1.3 63.4 + - - +
652D GLU* 3.3 6.5 + - - +
653D LEU* 3.1 31.0 + - + +
721D LEU* 5.2 4.3 - - + +
725D MET* 3.9 29.4 - - + -
728D VAL* 4.2 6.1 - - + -
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Residues in contact with SER 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609D GLY* 3.6 23.3 - - - -
612D SER* 3.0 27.3 - - - -
613D TYR* 3.3 9.0 + - - +
618D ALA* 3.1 30.5 - - - +
621D LEU* 4.6 2.5 - - - -
646D MET 3.3 7.6 + - - -
647D LEU* 3.2 12.7 + - - -
649D VAL* 1.3 79.8 - - - +
651D SER* 1.3 62.7 + - - +
653D LEU* 3.4 1.8 + - - -
654D HIS 3.2 13.9 + - - -
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Residues in contact with SER 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D ALA* 3.6 14.3 - - - +
647D LEU 2.8 13.4 + - - -
648D TYR* 3.3 13.0 - - - -
650D SER* 1.3 77.6 - - - +
652D GLU* 1.3 62.5 + - - +
654D HIS* 3.1 7.7 + - - +
655D ARG* 2.8 29.4 + - - +
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Residues in contact with GLU 652 (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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648D TYR* 3.0 51.6 + - + +
649D VAL 3.3 8.0 + - - +
651D SER* 1.3 81.8 + - - +
653D LEU* 1.3 57.1 + - - +
655D ARG* 3.3 42.4 + - - +
656D LEU* 3.0 36.0 + - - +
721D LEU* 4.0 28.4 - - + +
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Residues in contact with LEU 653 (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 PHE* 4.1 26.2 - - + +
609D GLY* 3.5 7.0 - - - -
610D TRP* 3.3 48.0 - - + +
613D TYR* 3.6 18.5 - - + -
649D VAL* 3.1 20.7 + - + +
650D SER 3.7 5.6 - - - +
652D GLU* 1.3 75.7 - - - +
654D HIS* 1.3 58.1 + - - +
657D GLN* 3.0 21.7 + - - -
658D VAL* 3.1 41.5 + - + -
663D TYR* 5.1 0.2 - - + -
666D MET* 4.8 0.2 - - + -
721D LEU* 3.9 16.4 - - + -
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Residues in contact with HIS 654 (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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613D TYR* 3.3 27.6 - - + -
617D SER* 3.7 35.7 + - - -
618D ALA* 3.9 9.2 - - + -
650D SER 3.2 8.1 + - - +
651D SER* 3.1 10.2 + - - +
653D LEU* 1.3 78.3 - - - +
655D ARG* 1.3 70.3 + - - +
657D GLN* 3.0 33.5 + - - +
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Residues in contact with ARG 655 (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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651D SER* 2.8 17.9 + - - +
652D GLU* 3.3 38.0 + - - +
654D HIS* 1.3 83.5 - - - +
656D LEU* 1.3 87.8 + - - +
657D GLN* 3.3 5.5 + - - +
717D GLN* 4.4 16.6 + - - +
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Residues in contact with LEU 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652D GLU* 3.0 18.6 + - - +
655D ARG* 1.3 119.7 - - - +
657D GLN* 1.3 68.1 + - - +
658D VAL* 4.0 11.4 - - + -
714D ARG* 2.7 36.7 + - - +
717D GLN* 4.0 41.1 - - + +
718D LEU* 4.0 22.0 - - + -
721D LEU* 4.5 15.7 - - + -
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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
------------------------------------------------------------
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