Contacts of the helix formed by residues 607 - 625 (chain T) in PDB entry 5IJ7
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 ASN 607 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B CYS* 4.0 9.8 - - - -
261B THR* 2.9 28.6 - - - +
262B PRO* 3.5 3.2 - - + +
263B ASN* 3.1 33.7 + - + +
605T ASP 4.1 0.2 + - - -
606T VAL* 1.3 75.4 - - - +
608T GLU* 1.3 59.8 + - - +
609T GLY 2.8 29.9 - - - +
610T GLU* 2.9 38.1 + - - +
611T LYS* 2.9 28.0 + - - +
655T ASN* 4.8 0.2 - - - +
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Residues in contact with GLU 608 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASN* 5.1 4.0 + - - +
601T GLU* 2.9 28.5 - - - +
606T VAL 4.4 2.8 - - - +
607T ASN* 1.3 73.7 - - - +
609T GLY* 1.3 59.8 + - - +
611T LYS* 3.3 23.6 + - - +
612T GLU* 3.4 23.4 + - - +
652T LEU* 4.6 1.0 - - - +
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Residues in contact with GLY 609 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASN* 3.7 15.1 - - - +
607T ASN* 2.8 17.7 - - - +
608T GLU* 1.3 70.7 - - - +
610T GLU* 1.3 61.1 + - - -
612T GLU 3.5 1.2 + - - -
613T VAL* 3.4 15.9 + - - +
652T LEU* 3.4 23.9 - - - +
655T ASN* 3.5 21.8 - - - -
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Residues in contact with GLU 610 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B THR* 4.9 5.6 - - - +
276B GLN 5.2 1.7 - - - +
277B SER 3.6 20.1 - - - +
280B SER* 2.9 37.4 + - - -
281B PHE* 3.6 26.1 - - + -
605T ASP 4.8 0.9 - - - +
606T VAL* 3.6 8.3 - - + +
607T ASN* 2.9 45.2 + - - +
609T GLY* 1.3 71.3 - - - +
611T LYS* 1.3 64.6 - - - +
613T VAL* 3.3 4.1 + - - +
614T MET* 3.0 32.2 + - + +
655T ASN* 3.7 11.2 + - - +
658T LEU* 5.3 0.7 - - - +
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Residues in contact with LYS 611 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600T ILE* 3.4 35.1 - - + +
601T GLU* 3.0 38.9 + - - +
603T PHE 2.9 29.2 + - - -
606T VAL* 3.3 27.7 + - + +
607T ASN 2.9 16.8 + - - +
608T GLU* 3.3 30.1 + - - +
610T GLU* 1.3 76.1 - - - +
612T GLU* 1.4 57.2 + - - +
614T MET* 3.3 4.1 + - - +
615T LYS* 3.0 35.8 + - - +
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Residues in contact with GLU 612 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601T GLU* 5.1 0.7 - - - +
608T GLU 3.4 15.7 + - - +
609T GLY 3.5 0.2 + - - -
610T GLU 3.4 0.2 - - - -
611T LYS* 1.4 75.9 - - - +
613T VAL* 1.3 63.3 + - - +
615T LYS* 3.7 30.5 + - - +
616T LEU* 3.2 40.7 + - + +
650T LYS* 3.6 33.6 + - + -
652T LEU* 3.7 24.0 - - + -
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Residues in contact with VAL 613 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 4.3 6.1 - - + -
609T GLY 3.4 12.9 + - - +
610T GLU 3.3 7.5 + - - +
611T LYS 3.3 0.6 - - - -
612T GLU* 1.3 75.0 - - - +
614T MET* 1.4 53.2 + - - +
616T LEU* 3.4 7.2 + - - +
617T TRP* 2.9 33.6 + - + +
639T PHE* 4.5 4.0 - - + -
647T ILE* 4.3 10.3 - - + -
652T LEU* 3.7 26.7 - - + +
655T ASN* 3.7 20.4 - - + +
656T PHE* 4.0 14.1 - - + +
659T HIS* 3.9 33.4 - - + +
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Residues in contact with MET 614 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER* 3.4 41.7 - - - +
281B PHE* 3.8 13.0 - - + +
284B LEU* 3.7 23.8 - - + -
292B TYR* 3.6 51.6 - - + -
600T ILE* 4.2 13.7 - - + -
606T VAL* 4.5 6.3 - - - -
610T GLU* 3.0 26.5 + - + +
611T LYS 3.5 4.3 - - - +
613T VAL* 1.4 72.7 - - - +
615T LYS* 1.4 58.8 + - - +
617T TRP* 3.4 1.8 + - - +
618T ASN* 3.0 36.8 + - - +
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Residues in contact with LYS 615 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596T THR* 5.9 0.4 - - - -
597T ILE* 3.5 53.0 + - + +
600T ILE* 3.9 19.7 - - + -
601T GLU* 2.8 41.5 + - - +
611T LYS 3.0 18.9 + - - +
612T GLU* 3.7 35.6 + - - +
614T MET* 1.4 73.7 - - - +
616T LEU* 1.3 60.4 - - + +
618T ASN* 3.4 5.9 + - - +
619T LEU* 3.0 37.6 + - + +
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Residues in contact with LEU 616 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612T GLU* 3.2 34.8 + - + +
613T VAL 3.6 4.0 - - - +
615T LYS* 1.3 77.4 - - + +
617T TRP* 1.3 64.7 + - - +
619T LEU* 3.5 14.8 + - + +
620T HIS* 3.1 23.4 + - - +
639T PHE* 3.4 15.0 - - + -
643T TYR* 3.7 26.4 - - + -
646T LYS* 4.4 21.5 - - + -
647T ILE* 3.8 24.9 - - + -
650T LYS* 5.0 4.9 - - + -
652T LEU* 4.5 9.9 - - + -
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Residues in contact with TRP 617 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PHE* 3.9 8.7 - - - -
290B PHE 2.9 26.9 + - - -
292B TYR* 3.8 27.1 - + + -
613T VAL* 2.9 17.8 + - + +
614T MET 3.8 3.6 - - - +
616T LEU* 1.3 74.6 - - - +
618T ASN* 1.3 62.1 + - - +
620T HIS* 3.2 12.2 + + - +
621T VAL* 2.9 40.0 + - + +
632T MET* 3.3 17.0 - - + -
635T ALA* 3.9 18.2 - - + -
636T CYS* 3.9 13.7 - - - -
639T PHE* 3.7 42.7 - + + -
659T HIS* 3.4 29.8 - + + +
663T MET* 3.3 22.9 - - + -
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Residues in contact with ASN 618 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LYS* 3.4 17.6 - - + +
292B TYR* 2.8 53.1 + - - +
293B ASP 5.0 0.2 + - - -
294B CYS* 6.0 0.2 - - - +
596T THR* 3.0 31.4 + - + +
600T ILE* 4.1 6.7 - - - +
614T MET 3.0 20.3 + - - +
615T LYS* 3.6 5.2 - - - +
617T TRP* 1.3 76.1 - - - +
619T LEU* 1.4 57.2 + - - +
621T VAL* 3.4 4.6 + - - +
622T MET* 2.9 39.5 + - - +
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Residues in contact with LEU 619 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588T ASP* 5.3 0.9 - - - +
593T ARG* 3.6 48.2 - - + +
596T THR* 4.4 4.9 - - + -
597T ILE* 4.0 17.9 - - + -
615T LYS* 3.0 29.6 + - + +
616T LEU* 3.8 17.7 - - + +
617T TRP 3.3 0.2 - - - -
618T ASN* 1.4 75.4 - - - +
620T HIS* 1.3 56.3 + - - +
622T MET* 3.9 5.5 - - - +
623T LYS* 3.2 28.2 + - - +
643T TYR* 3.9 14.4 + - + +
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Residues in contact with HIS 620 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616T LEU 3.1 13.7 + - - +
617T TRP* 3.3 20.9 - + - +
619T LEU* 1.3 73.8 - - - +
621T VAL* 1.3 65.5 + - + +
623T LYS* 3.3 4.5 + - - +
624T HIS* 3.1 57.2 + + - -
626T PHE* 3.7 17.1 - + - -
635T ALA 2.8 25.8 + - - -
638T LEU* 3.7 14.4 - - + -
639T PHE* 3.6 34.5 + + + -
642T ASN* 4.3 1.3 + - - -
643T TYR* 3.6 27.2 + - + -
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Residues in contact with VAL 621 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B CYS 4.1 6.3 - - - +
290B PHE* 3.6 15.3 - - + +
291B LYS* 3.9 30.7 + - + +
617T TRP* 2.9 56.6 + - + +
618T ASN 4.0 3.4 - - - +
620T HIS* 1.3 73.8 - - + +
622T MET* 1.3 53.1 + - - +
625T GLY* 2.8 33.3 + - - -
626T PHE* 3.7 34.2 + - + +
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Residues in contact with MET 622 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B LYS* 4.1 26.2 - - + +
295B PHE* 5.2 4.0 - - - -
587T LYS* 4.1 6.9 - - - +
588T ASP* 3.1 31.7 - - + +
592T LEU* 3.8 21.3 - - + +
593T ARG* 3.6 42.8 - - + +
596T THR* 3.8 24.0 - - - -
618T ASN* 2.9 23.8 + - - +
619T LEU* 3.9 6.3 - - - +
621T VAL* 1.3 74.2 - - - +
623T LYS* 1.4 61.8 + - - +
625T GLY* 3.8 6.6 + - - -
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Residues in contact with LYS 623 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587T LYS* 3.4 22.0 + - - +
588T ASP* 3.6 24.1 - - - +
593T ARG* 5.8 6.4 - - - +
619T LEU 3.2 19.1 + - - +
620T HIS* 3.3 7.4 + - - +
622T MET* 1.4 75.6 - - - +
624T HIS* 1.4 75.2 + - + +
643T TYR* 5.2 8.1 - - - +
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Residues in contact with HIS 624 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587T LYS* 3.5 12.6 + - - +
620T HIS* 3.1 50.8 + + - -
623T LYS* 1.4 93.9 - - + +
625T GLY* 1.3 65.4 + - - +
626T PHE* 3.4 31.4 + + + -
638T LEU* 3.6 19.0 - - + +
642T ASN* 3.8 13.1 + - - -
643T TYR* 5.7 1.3 - + - -
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Residues in contact with GLY 625 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LYS* 6.2 0.9 - - - -
587T LYS* 3.9 13.2 + - - +
621T VAL 2.8 16.1 + - - -
622T MET* 3.8 3.9 + - - -
623T LYS 3.6 2.0 - - - -
624T HIS* 1.3 78.8 - - - +
626T PHE* 1.3 64.2 - - - -
627T ILE* 3.4 17.4 + - - +
631T GLN* 4.8 0.9 + - - +
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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