Contacts of the helix formed by residues 629 - 647 (chain D) in PDB entry 4YJL
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 LEU 629 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627D ASN 5.7 0.7 - - - +
628D THR* 1.3 80.5 - - - +
630D ALA* 1.3 63.9 + - - +
631D ILE 3.3 2.7 - - - -
632D ILE* 3.2 26.1 + - + +
633D GLU* 2.9 37.3 + - - +
671D SER* 4.9 2.9 - - - +
672D HIS* 6.1 1.3 - - + +
673D SER* 3.9 26.2 - - - +
676D ILE* 4.1 12.3 - - + -
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Residues in contact with ALA 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D LYS* 4.1 34.1 - - + -
628D THR* 3.5 7.3 + - - +
629D LEU* 1.3 76.9 - - - +
631D ILE* 1.3 57.7 + - - +
633D GLU* 3.6 12.2 + - - +
634D SER* 2.8 35.3 + - - -
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Residues in contact with ILE 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582D GLU* 4.0 14.6 - - + +
585D LEU* 3.7 24.2 - - + +
586D LYS* 3.5 41.5 - - + +
589D LEU* 4.0 12.7 - - + +
619D THR* 4.1 8.9 - - - +
622D TYR* 3.5 55.6 - - + -
624D SER* 5.9 0.4 - - - -
628D THR 5.5 0.4 + - - -
629D LEU 3.3 0.6 - - - -
630D ALA* 1.3 72.2 - - - +
632D ILE* 1.3 57.6 + - - +
634D SER* 3.4 3.3 + - - +
635D GLY* 2.8 32.7 + - - -
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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
----------------------------------------------------------
619D THR 3.5 19.5 - - - +
620D LEU* 3.8 12.6 - - - +
621D THR* 4.9 1.1 - - - -
622D TYR* 3.6 27.6 - - + +
628D THR 5.8 0.4 - - - +
629D LEU* 3.2 28.9 + - + +
631D ILE* 1.3 74.6 - - - +
633D GLU* 1.3 54.8 + - - +
636D GLY* 2.8 31.4 + - - -
668D HIS* 3.5 32.5 - - + +
676D ILE* 3.8 21.2 - - + +
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Residues in contact with GLU 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593D TRP* 3.7 8.3 - - + -
629D LEU* 2.9 29.4 + - - +
630D ALA* 3.6 12.1 + - - +
632D ILE* 1.3 76.0 - - - +
634D SER* 1.3 57.6 + - - +
637D GLY* 2.9 22.7 + - - -
673D SER* 2.7 25.2 + - - -
675D THR* 3.8 25.3 + - + +
676D ILE* 3.5 20.9 - - + -
679D ASN* 3.0 14.4 + - - +
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Residues in contact with SER 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D LYS* 4.6 3.1 + - - -
589D LEU* 3.3 32.2 - - - +
590D SER* 4.1 9.6 + - - -
593D TRP* 3.5 23.1 - - - -
630D ALA 2.8 27.2 + - - -
631D ILE* 3.4 8.0 + - - +
633D GLU* 1.3 71.5 - - - +
635D GLY* 1.3 67.7 + - - +
637D GLY* 3.3 0.7 + - - -
638D ILE* 3.0 32.3 + - - +
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Residues in contact with GLY 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589D LEU* 4.1 8.4 - - - +
616D LEU* 4.4 6.8 - - - +
619D THR* 3.3 27.7 + - - -
620D LEU* 4.5 1.6 - - - -
631D ILE 2.8 18.5 + - - -
634D SER* 1.3 75.6 + - - +
636D GLY* 1.3 58.7 + - - +
638D ILE* 3.5 8.3 + - - +
639D LEU* 3.1 22.7 + - - +
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Residues in contact with GLY 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D LEU* 3.6 22.6 - - - +
632D ILE 2.8 23.6 + - - -
633D GLU 3.8 0.7 - - - -
635D GLY* 1.3 71.4 - - - -
637D GLY* 1.3 55.6 + - - +
639D LEU* 3.7 3.2 - - - +
640D ARG* 2.9 29.8 + - - +
665D LEU* 6.4 0.7 - - - -
668D HIS* 5.5 2.2 - - - -
679D ASN* 3.8 12.8 - - - +
683D THR* 4.3 2.3 + - - -
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Residues in contact with GLY 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593D TRP* 3.3 29.3 + - - -
633D GLU 2.9 11.3 + - - -
634D SER 3.3 0.6 + - - -
635D GLY 3.2 0.4 - - - -
636D GLY* 1.3 73.1 - - - +
638D ILE* 1.3 64.2 + - - +
640D ARG* 3.4 3.9 + - - +
641D ASN* 3.0 27.5 + - - +
679D ASN* 3.3 17.7 - - - +
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Residues in contact with ILE 638 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573D MET* 5.7 0.9 - - - -
589D LEU* 3.5 40.4 - - + +
592D LEU* 3.7 14.6 - - + +
593D TRP* 3.5 22.1 - - - +
596D SER* 4.1 10.3 - - - -
606D ILE* 4.2 24.0 - - + -
616D LEU* 3.8 30.7 - - + -
634D SER 3.0 18.2 + - - +
635D GLY 3.7 3.8 - - - +
637D GLY* 1.3 74.2 - - - +
639D LEU* 1.3 58.6 + - - +
641D ASN* 3.1 2.6 + - - +
642D VAL* 2.9 31.7 + - + +
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Residues in contact with LEU 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613D LEU* 4.9 2.9 - - + -
616D LEU* 4.7 16.1 - - + +
617D VAL* 4.6 13.2 - - + -
620D LEU* 3.7 24.5 - - + -
635D GLY 3.1 14.6 + - - +
636D GLY* 3.7 5.8 - - - +
637D GLY 3.3 0.2 - - - -
638D ILE* 1.3 77.6 - - - +
640D ARG* 1.3 57.8 + - - +
642D VAL* 3.3 7.7 + - + +
643D SER* 2.8 34.0 + - - -
646D ILE* 3.9 23.3 - - + -
656D LEU* 4.4 11.2 - - + -
661D CYS* 3.7 27.8 - - - -
665D LEU* 4.6 3.6 - - + -
683D THR* 4.2 15.0 - - + +
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Residues in contact with ARG 640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636D GLY 2.9 17.9 + - - +
637D GLY* 3.4 4.3 - - - +
639D LEU* 1.3 74.5 - - - +
641D ASN* 1.3 72.1 + - - +
643D SER* 2.7 22.0 + - - -
678D SER* 3.6 28.5 + - - -
679D ASN* 3.3 32.7 + - + +
682D GLY* 4.0 13.6 - - - -
683D THR* 3.3 22.3 + - - +
685D TRP* 6.0 0.6 - - - -
686D ASN* 4.0 5.2 + - - +
717D MET* 4.1 24.0 - - - +
496I PRO* 4.4 9.4 - - + +
497I ARG 3.0 29.4 + - - +
499I SER* 3.4 28.7 + - - +
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Residues in contact with ASN 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593D TRP* 3.2 9.9 + - - -
596D SER* 2.8 37.5 + - - +
597D ALA* 3.5 10.5 - - - +
603D LYS* 3.1 22.7 - - - -
637D GLY 3.0 15.0 + - - +
638D ILE 3.6 2.7 - - - +
640D ARG* 1.3 81.8 - - - +
642D VAL* 1.3 58.9 + - - +
644D SER* 3.3 9.7 + - - -
498I ASP* 3.3 22.0 - - - +
499I SER* 2.9 43.6 + - - -
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Residues in contact with VAL 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596D SER* 4.3 4.0 - - - -
603D LYS* 3.9 34.5 - - + +
606D ILE* 4.0 24.7 - - + -
607D CYS* 4.0 15.5 - - - -
613D LEU* 4.3 8.7 - - + -
616D LEU* 4.8 4.7 - - + -
638D ILE* 2.9 26.2 + - + +
639D LEU* 3.6 11.4 - - - +
641D ASN* 1.3 69.4 - - - +
643D SER* 1.3 60.9 + - - +
644D SER 3.1 3.4 - - - -
645D LEU* 2.9 22.2 + - - +
646D ILE* 3.1 28.0 + - + +
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Residues in contact with SER 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D LEU 2.8 16.4 + - - -
640D ARG 2.7 18.5 + - - -
642D VAL* 1.3 76.3 - - - +
644D SER* 1.3 56.0 + - - +
645D LEU 3.2 0.2 - - - -
646D ILE* 3.7 15.8 - - - +
647D ALA* 2.9 31.4 + - - +
656D LEU* 6.1 0.2 - - - -
683D THR* 3.8 27.7 - - - -
686D ASN* 2.8 30.1 + - - +
687D LEU* 4.6 6.1 - - - +
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Residues in contact with SER 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600D THR* 5.8 1.0 - - - +
603D LYS* 3.4 18.8 - - - +
641D ASN 3.3 16.5 + - - -
643D SER* 1.3 81.8 + - - +
645D LEU* 1.3 62.6 + - - +
647D ALA* 4.0 9.9 + - - +
648D THR* 4.3 8.7 + - - +
686D ASN* 3.4 22.5 - - - +
496I PRO* 6.0 2.7 - - - -
498I ASP* 5.8 1.1 - - - -
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Residues in contact with LEU 645 (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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600D THR* 3.7 20.2 - - + +
603D LYS* 3.7 13.0 - - + +
604D ALA* 3.4 42.4 - - + +
607D CYS* 4.7 9.2 - - + -
642D VAL 2.9 9.8 + - - +
644D SER* 1.3 78.0 + - - +
646D ILE* 1.3 65.1 + - - +
647D ALA 3.1 1.8 - - - -
648D THR* 3.2 25.4 + - - +
649D ASN* 3.6 10.3 + - + +
652D HIS* 5.8 0.9 - - - +
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Residues in contact with ILE 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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607D CYS* 4.2 7.6 - - - -
613D LEU* 3.8 27.6 - - + -
639D LEU* 3.9 17.7 - - + -
642D VAL* 3.1 30.7 + - + +
643D SER* 3.4 14.8 + - - +
645D LEU* 1.3 74.9 - - - +
647D ALA* 1.3 58.3 + - - +
649D ASN* 2.9 36.0 + - - +
652D HIS* 4.0 7.0 - - + -
653D ARG* 3.6 24.3 - - - +
656D LEU* 3.9 24.9 - - + -
687D LEU* 4.2 8.3 - - + -
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Residues in contact with ALA 647 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643D SER 2.9 17.2 + - - +
644D SER* 4.0 8.3 - - - +
645D LEU 3.1 0.6 - - - -
646D ILE* 1.3 75.8 - - - +
648D THR* 1.3 62.4 + - + +
649D ASN 3.4 0.2 - - - -
653D ARG* 2.9 32.4 + - - +
686D ASN* 3.4 30.7 - - + +
687D LEU* 4.5 2.9 - - + -
689D ALA* 5.2 2.2 - - + +
804D EDO 3.1 15.4 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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