Contacts of the helix formed by residues 628 - 643 (chain D) in PDB entry 5ED1
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 628 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A LEU* 4.6 1.1 - - - -
387D GLY 3.6 16.2 - - - +
388D LEU* 3.9 24.2 - - - +
389D ALA 4.1 4.9 - - - +
390D LEU* 3.7 16.7 - - + +
401D ARG* 3.9 1.1 - - - -
624D ALA* 4.2 9.0 - - - -
625D SER 3.4 20.0 + - - +
626D ARG 3.6 0.2 - - - -
627D LEU* 1.3 82.0 - - - +
629D LYS* 1.3 66.4 + - - +
630D HIS* 3.6 6.3 - - - -
631D ALA* 3.0 26.7 + - - -
632D LEU* 3.0 12.5 + - - +
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Residues in contact with LYS 629 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D GLY* 3.5 13.6 + - - +
389D ALA 5.1 6.2 + - - +
391D ASN* 3.8 15.5 - - - +
401D ARG* 3.8 6.5 - - - +
628D CYS* 1.3 73.3 - - - +
630D HIS* 1.3 57.5 + - - +
632D LEU* 3.5 2.7 + - - +
633D TYR* 2.9 30.7 + - - +
658D TYR* 3.7 14.4 - - + +
662D LYS* 3.7 2.4 - - - +
690D LYS* 6.4 0.2 - - - -
694D GLN* 3.7 35.1 - - - +
695D ASP* 3.1 25.9 + - - +
697D PHE* 3.7 15.7 - - + -
801D IHP 2.5 57.3 + - - +
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Residues in contact with HIS 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 3.7 23.9 - - + +
316A GLN 4.4 13.6 + - - -
317A LEU* 4.7 13.4 - - + +
386D ARG* 3.6 19.0 + - + +
387D GLY 3.2 13.2 + - - +
388D LEU* 3.9 18.0 - - + +
628D CYS* 3.1 3.1 - - - -
629D LYS* 1.3 80.0 - - - +
631D ALA* 1.3 58.5 + - - +
633D TYR* 3.5 2.1 + - - +
634D CYS* 3.0 26.6 + - + +
697D PHE* 3.9 13.5 - - - -
698D SER 3.7 15.9 - - - -
699D LEU* 3.3 30.8 - - + +
700D THR 5.0 0.8 + - - -
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Residues in contact with ALA 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 4.2 16.8 - - + +
625D SER 3.5 18.6 - - - +
626D ARG* 3.3 27.8 - - - +
628D CYS* 3.0 11.7 + - - +
630D HIS* 1.3 76.7 - - - +
632D LEU* 1.3 61.0 + - - +
634D CYS* 3.1 9.5 - - - +
635D ARG* 3.0 31.0 + - - +
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Residues in contact with LEU 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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401D ARG* 3.6 36.6 - - + +
404D LEU* 4.0 26.7 - - + -
405D ARG* 4.1 25.1 - - + -
408D TYR* 4.0 24.3 + - + +
532D LEU* 5.5 3.6 - - + -
626D ARG 4.2 8.5 - - - +
627D LEU* 3.9 7.9 - - - +
628D CYS 3.0 15.3 + - - +
629D LYS* 3.9 4.5 - - - +
631D ALA* 1.3 72.7 - - - +
633D TYR* 1.3 62.1 + - - +
635D ARG* 3.3 7.0 + - + +
636D TRP* 2.9 30.9 + - - +
658D TYR* 5.2 4.7 - - - +
801D IHP 4.9 5.6 - - - +
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Residues in contact with TYR 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532D LEU* 4.0 9.9 - - + -
629D LYS 2.9 19.9 + - - +
630D HIS* 3.7 6.5 - - - +
632D LEU* 1.3 76.6 - - - +
634D CYS* 1.3 57.9 + - - +
636D TRP* 3.5 15.0 - + - +
637D MET* 2.9 60.8 + - + +
655D PRO 3.9 1.6 - - - -
656D ASN 3.5 24.8 + - - -
657D VAL 3.7 3.3 - - - -
658D TYR* 3.5 40.1 - + + -
661D SER* 2.7 36.5 + - - -
697D PHE* 4.2 10.3 - + - -
699D LEU* 3.5 26.0 - - + -
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Residues in contact with CYS 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 4.5 19.7 - - + -
630D HIS* 3.0 16.0 + - + +
631D ALA* 3.1 13.9 - - - +
632D LEU 3.1 0.2 - - - -
633D TYR* 1.3 75.8 - - - +
635D ARG* 1.3 64.9 + - + +
637D MET* 3.3 4.5 + - - +
638D ARG* 3.1 34.9 + - - +
699D LEU* 4.1 16.1 - - + +
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Residues in contact with ARG 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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405D ARG* 3.7 34.6 + - + +
408D TYR* 3.4 30.0 - - + +
409D THR* 3.0 49.5 + - - +
412D GLU* 3.6 18.2 + - - +
626D ARG 6.1 0.9 - - - +
631D ALA 3.0 18.1 + - - +
632D LEU* 3.3 11.2 + - + +
634D CYS* 1.3 77.4 - - + +
636D TRP* 1.3 61.8 + - - +
638D ARG* 3.1 39.4 + - - +
639D VAL* 3.0 24.4 + - - +
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Residues in contact with TRP 636 (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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408D TYR* 3.1 32.4 - + - +
532D LEU* 3.1 40.5 + - + -
533D LEU 4.3 0.2 - - - -
535D ILE* 3.7 23.8 - - + -
536D PHE* 3.4 30.5 - + - -
632D LEU 2.9 17.1 + - - +
633D TYR* 3.5 24.5 - + + +
635D ARG* 1.3 73.4 - - - +
637D MET* 1.3 71.7 + - - +
639D VAL* 3.2 4.2 + - - +
640D HIS* 2.8 51.0 + + + -
652D ILE* 3.9 15.7 - - + -
655D PRO* 4.0 21.8 - - + -
661D SER* 4.6 5.4 - - - -
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Residues in contact with MET 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633D TYR* 2.9 58.3 + - + +
634D CYS* 3.6 5.4 - - - +
636D TRP* 1.3 91.0 - - + +
638D ARG* 1.3 63.9 + - - +
640D HIS* 3.2 7.7 + - - +
641D GLY* 3.0 19.4 + - - -
655D PRO* 3.8 26.0 - - + +
656D ASN 5.1 0.9 - - - +
699D LEU* 3.5 23.6 - - + -
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Residues in contact with ARG 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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412D GLU* 3.0 33.3 + - - +
634D CYS* 3.1 26.6 + - - +
635D ARG* 3.1 37.8 + - - +
637D MET* 1.3 77.2 - - - +
639D VAL* 1.3 63.0 + - - +
641D GLY* 3.1 4.6 + - - -
642D LYS* 3.0 33.4 + - + +
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Residues in contact with VAL 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D TYR* 4.0 33.7 - - + +
411D LEU* 4.3 13.2 - - + -
412D GLU* 4.3 15.5 - - + +
415D LEU* 4.4 6.5 - - + -
536D PHE* 3.4 31.4 - - + -
635D ARG 3.0 16.7 + - - +
636D TRP 3.5 7.6 - - - +
638D ARG* 1.3 76.1 - - - +
640D HIS* 1.3 57.3 + - - +
642D LYS* 2.8 25.3 + - - +
643D VAL* 2.9 26.6 + - + +
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Residues in contact with HIS 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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536D PHE* 3.9 18.6 - + + -
636D TRP* 2.8 47.9 + + + +
637D MET* 3.2 12.7 + - - +
639D VAL* 1.3 75.5 - - - +
641D GLY* 1.3 63.2 + - - +
643D VAL* 3.4 20.8 - - - +
648D LEU* 4.2 16.4 - - + +
652D ILE* 3.6 25.4 + - + +
653D THR 4.5 5.4 - - - -
655D PRO* 4.0 22.2 - - + +
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Residues in contact with GLY 641 (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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637D MET 3.0 13.4 + - - -
638D ARG* 3.1 5.1 + - - -
639D VAL 3.0 0.4 - - - -
640D HIS* 1.3 81.3 + - - +
642D LYS* 1.3 60.4 + - - +
643D VAL 3.5 1.6 + - - +
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Residues in contact with LYS 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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412D GLU* 4.2 38.6 - - + +
415D LEU* 3.7 38.5 + - + +
416D ASN* 4.3 15.7 + - - +
638D ARG* 3.0 24.9 + - + +
639D VAL* 2.8 12.4 + - - +
641D GLY* 1.3 73.9 - - - +
643D VAL* 1.3 59.2 + - - +
644D PRO* 3.5 10.1 - - - +
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Residues in contact with VAL 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D LEU* 6.2 0.4 - - + -
415D LEU* 3.5 26.2 - - + -
434D PHE* 5.0 8.1 - - + -
536D PHE* 4.5 8.1 - - + -
639D VAL* 2.9 30.0 + - + +
640D HIS* 3.4 16.8 + - - +
641D GLY 3.3 2.8 - - - +
642D LYS* 1.3 77.4 - - - +
644D PRO* 1.3 81.2 - - + +
645D SER* 3.6 2.8 + - - -
647D LEU* 4.2 16.8 - - + +
648D LEU* 3.9 23.7 - - + +
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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