Contacts of the helix formed by residues 673 - 688 (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 SER 673 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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629D LEU* 3.9 13.6 - - - +
633D GLU* 2.7 28.2 + - - -
671D SER* 3.0 10.4 + - - -
672D HIS* 1.3 77.3 - - - +
674D LEU* 1.3 63.5 + - - +
675D THR* 3.5 4.0 + - - -
676D ILE* 3.3 24.7 + - - +
677D VAL* 3.1 25.7 + - - +
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Residues in contact with LEU 674 (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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672D HIS 3.5 7.6 + - - +
673D SER* 1.3 73.2 + - - +
675D THR* 1.3 56.9 + - - +
677D VAL* 4.6 3.6 - - + -
678D SER* 2.9 33.1 + - - -
713D SER* 5.7 0.9 - - - +
715D HIS* 4.1 29.1 - - + +
718D ILE* 3.7 24.0 - - + +
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Residues in contact with THR 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593D TRP* 3.6 31.4 - - + -
633D GLU* 3.8 22.4 + - + +
673D SER* 3.2 9.1 + - - -
674D LEU* 1.3 79.1 - - - +
676D ILE* 1.3 55.5 + - - +
678D SER* 3.5 5.1 + - - -
679D ASN* 2.9 42.1 + - - +
715D HIS* 5.9 1.1 - - - -
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Residues in contact with ILE 676 (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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629D LEU* 4.1 21.5 - - + -
632D ILE* 3.8 24.5 - - + -
633D GLU* 3.5 24.9 - - + -
668D HIS* 3.6 36.7 + - + +
671D SER* 3.7 27.6 - - - +
673D SER* 3.2 19.7 + - - +
675D THR* 1.3 74.3 - - - +
677D VAL* 1.3 59.8 + - - +
679D ASN* 3.4 7.2 + - - +
680D ALA* 2.9 29.1 + - - +
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Residues in contact with VAL 677 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668D HIS 3.5 18.8 - - - +
669D LEU* 3.9 12.3 - - - +
671D SER* 3.4 22.9 - - - +
673D SER 3.1 16.9 + - - +
674D LEU* 3.9 6.1 - - + +
676D ILE* 1.3 74.5 - - - +
678D SER* 1.3 58.3 + - - +
680D ALA* 3.2 5.2 + - - +
681D CYS* 2.9 29.8 + - - -
710D LEU* 3.9 30.5 - - + -
718D ILE* 3.8 25.6 - - + -
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Residues in contact with SER 678 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640D ARG* 3.6 13.9 + - - -
674D LEU 2.9 20.2 + - - -
675D THR* 3.7 6.1 - - - -
677D VAL* 1.3 76.7 - - - +
679D ASN* 1.3 64.1 + - - +
681D CYS* 3.3 6.4 + - - +
682D GLY* 3.1 17.7 + - - -
715D HIS* 3.6 15.1 + - - -
717D MET* 3.2 30.0 - - - +
718D ILE* 3.8 10.7 - - - +
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Residues in contact with ASN 679 (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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593D TRP* 3.7 9.2 - - - -
633D GLU* 3.0 28.9 + - - +
636D GLY* 3.8 16.5 - - - +
637D GLY* 3.3 14.1 - - - +
640D ARG* 3.3 15.2 + - + +
665D LEU* 5.5 0.2 - - - -
668D HIS* 6.4 0.2 - - - +
675D THR* 2.9 27.9 + - - +
676D ILE* 3.7 5.3 - - - +
678D SER* 1.3 75.4 - - - +
680D ALA* 1.3 63.6 + - - +
682D GLY 3.2 2.1 + - - -
683D THR* 3.0 27.2 + - - -
499I SER* 2.9 25.6 + - - -
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Residues in contact with ALA 680 (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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665D LEU* 3.7 28.5 - - + +
668D HIS* 3.7 26.2 + - + +
669D LEU* 3.9 8.5 - - + -
676D ILE 2.9 19.1 + - - +
677D VAL* 3.2 5.6 + - - +
679D ASN* 1.3 75.3 - - - +
681D CYS* 1.3 56.7 + - - +
683D THR* 3.2 2.4 + - - -
684D LEU* 2.8 36.2 + - - +
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Residues in contact with CYS 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669D LEU* 3.8 18.8 - - - -
677D VAL* 2.9 21.2 + - - -
678D SER* 3.6 8.7 - - - +
680D ALA* 1.3 74.4 - - - +
682D GLY* 1.3 57.5 + - - +
684D LEU* 3.8 5.5 - - - +
685D TRP* 2.8 32.2 + - - +
707D LEU* 5.0 2.0 - - - -
710D LEU* 3.9 17.3 - - - -
717D MET 4.5 4.0 - - - +
718D ILE* 4.0 9.9 - - - +
721D GLY* 3.9 11.8 - - - +
722D SER* 3.8 30.5 - - - +
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Residues in contact with GLY 682 (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 ARG* 4.0 26.5 - - - -
678D SER 3.1 13.1 + - - -
679D ASN 3.2 3.8 + - - -
681D CYS* 1.3 77.6 - - - +
683D THR* 1.3 60.3 + - - +
685D TRP* 3.2 11.5 - - - +
686D ASN* 3.2 25.8 + - - -
721D GLY* 4.9 1.1 - - - -
496I PRO* 3.8 9.1 - - - +
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Residues in contact with THR 683 (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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636D GLY 4.3 2.4 + - - -
639D LEU* 4.2 18.1 - - + +
640D ARG* 3.3 18.2 + - - +
643D SER* 3.8 22.7 - - - -
656D LEU* 5.5 0.2 - - + -
665D LEU* 3.6 30.1 - - + +
679D ASN 3.0 14.8 + - - -
680D ALA 3.7 5.4 - - - -
682D GLY* 1.3 74.8 - - - +
684D LEU* 1.3 59.0 + - - +
686D ASN* 3.2 4.0 + - - +
687D LEU* 2.8 45.2 + - + +
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Residues in contact with LEU 684 (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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662D LEU* 4.4 8.5 - - + +
665D LEU* 3.9 31.9 - - + +
666D LEU* 3.9 20.9 - - + -
669D LEU* 3.9 27.4 - - + -
680D ALA 2.8 21.0 + - - +
681D CYS* 3.8 3.8 - - - +
683D THR* 1.3 72.7 - - - +
685D TRP* 1.3 53.9 + - - +
687D LEU* 4.4 2.2 - - - +
688D SER* 2.7 43.3 + - - -
698D LEU* 3.7 33.0 - - + -
707D LEU* 4.5 9.0 - - + -
725D ALA* 4.0 12.1 - - + -
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Residues in contact with TRP 685 (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 ARG* 6.0 0.7 - - - -
681D CYS 2.8 14.3 + - - +
682D GLY* 3.2 13.9 - - - +
684D LEU* 1.3 74.5 - - - +
686D ASN* 1.3 62.9 + - - +
688D SER* 3.0 17.6 + - - -
689D ALA* 3.5 5.6 + - + +
720D MET* 4.0 38.1 - - + -
721D GLY* 3.7 22.7 - - - +
724D ALA* 3.3 27.1 - - + +
725D ALA* 3.9 8.4 - - - +
727D ARG* 5.5 2.5 - - - -
728D ASN* 3.2 16.9 + - - +
496I PRO* 3.5 47.3 - - + +
497I ARG 5.1 1.1 - - - -
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Residues in contact with ASN 686 (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 ARG 4.0 4.6 + - - -
643D SER* 2.8 40.8 + - - +
644D SER* 3.4 27.4 - - - +
647D ALA* 3.4 18.2 - - + +
653D ARG* 3.6 1.2 + - - -
682D GLY 3.2 4.0 + - - -
683D THR 3.2 4.0 + - - +
685D TRP* 1.3 80.4 - - - +
687D LEU* 1.3 61.7 + - - +
689D ALA* 3.2 20.2 + - - +
496I PRO* 3.3 35.3 - - - +
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Residues in contact with LEU 687 (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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643D SER* 4.6 7.4 - - - +
646D ILE* 4.2 24.9 - - + -
647D ALA* 4.5 6.5 - - - +
653D ARG* 2.8 42.3 + - + +
656D LEU* 3.8 20.9 - - + -
661D CYS* 4.5 0.9 - - - -
662D LEU* 3.9 31.9 - - + -
665D LEU* 4.0 8.7 - - + -
683D THR* 2.8 42.8 + - + +
684D LEU* 4.2 2.7 - - - +
686D ASN* 1.3 73.2 - - - +
688D SER* 1.3 61.1 + - - +
689D ALA 4.1 0.5 - - - +
691D ASN* 4.2 1.4 - - - +
694D ASP* 3.8 11.5 - - - +
698D LEU* 5.1 0.7 - - - -
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Residues in contact with SER 688 (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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684D LEU 2.7 26.8 + - - -
685D TRP 3.0 1.6 + - - -
687D LEU* 1.3 72.7 - - - +
689D ALA* 1.3 58.5 + - - +
695D GLN* 2.9 32.1 - - - +
698D LEU* 3.9 23.9 - - - +
725D ALA* 3.6 13.4 - - - -
728D ASN* 3.0 33.2 + - - +
729D LEU* 4.2 10.1 - - - -
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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