Contacts of the helix formed by residues 711 - 723 (chain B) in PDB entry 5M64
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 GLN 711 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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942A GLN* 4.4 8.5 + - - -
986A PHE* 5.0 0.4 - - + -
995A TYR* 5.7 0.2 - - - -
998A HIS* 3.5 18.5 + - + +
710B ASN* 1.3 77.1 - - - +
712B SER* 1.3 61.1 + - - +
713B PRO* 3.4 11.4 - - + +
714B ARG* 3.1 40.0 + - + +
715B ASN* 3.0 30.7 + - - -
956B SER 4.4 6.3 + - - +
957B ARG 3.9 2.6 - - - +
958B MET* 3.3 56.5 + - + +
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Residues in contact with SER 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995A TYR* 5.6 0.6 - - - -
998A HIS* 3.1 35.4 + - - -
999A CYS* 3.2 24.4 + - - -
1002A GLY* 3.5 5.9 - - - -
711B GLN* 1.3 68.0 - - - +
713B PRO* 1.3 69.3 - - - +
714B ARG 3.0 1.3 - - - -
715B ASN* 2.8 27.1 + - - +
716B MET* 2.9 39.7 + - - +
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Residues in contact with PRO 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998A HIS* 4.2 5.4 - - + -
1002A GLY* 3.8 26.4 - - - +
1005A GLY* 6.1 1.3 - - - -
1006A LEU* 4.8 11.6 - - + +
711B GLN* 3.7 15.0 - - + +
712B SER* 1.3 92.8 - - - +
714B ARG* 1.3 80.1 + - - +
716B MET* 4.1 1.5 - - + +
717B TYR* 3.0 27.9 + - - +
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Residues in contact with ARG 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710B ASN* 4.7 2.5 - - + -
711B GLN* 3.1 51.4 + - + +
712B SER 3.0 0.6 - - - -
713B PRO* 1.3 101.3 + - - +
715B ASN* 1.3 61.8 + - - +
717B TYR* 3.7 18.3 - - - +
718B GLN* 2.9 31.4 + - - +
921B HIS 3.6 17.6 - - - +
922B GLY* 3.8 7.7 - - - -
956B SER 4.7 2.2 + - - -
957B ARG* 3.4 57.2 + - - +
958B MET 5.1 1.1 - - - +
959B THR* 4.0 10.1 - - + -
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Residues in contact with ASN 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995A TYR* 2.6 39.9 + - - -
999A CYS* 4.7 1.4 - - - -
531B VAL* 3.6 16.7 - - + +
704B THR* 5.7 3.1 - - - +
707B SER* 4.2 13.9 + - - +
710B ASN* 4.4 8.3 + - - +
711B GLN 3.0 19.7 + - - +
712B SER* 2.8 17.8 + - - +
714B ARG* 1.3 76.9 - - - +
716B MET* 1.3 73.3 + - + +
718B GLN* 3.8 5.4 - - - +
719B CYS* 2.9 28.9 + - - +
921B HIS 5.4 0.9 - - - +
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Residues in contact with MET 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999A CYS* 4.8 2.0 - - - +
1002A GLY 4.7 0.4 - - - -
1003A ARG* 4.1 27.1 - - + +
1006A LEU* 4.4 26.7 - - + -
530B PRO 3.9 6.7 - - - +
531B VAL* 3.2 35.9 - - + +
533B THR* 3.7 32.8 - - + +
534B PRO 5.0 1.8 - - - -
535B ASP* 5.2 3.6 + - - +
712B SER* 2.9 44.8 + - - +
713B PRO 4.4 2.7 - - - +
715B ASN* 1.3 85.2 - - + +
717B TYR* 1.3 62.8 + - - +
718B GLN 3.4 0.2 + - - -
719B CYS* 3.4 13.3 + - - +
720B GLN* 3.8 9.9 + - - +
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Residues in contact with TYR 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A ASP* 2.8 39.5 + - - +
535B ASP* 5.2 15.3 - - + -
713B PRO 3.0 22.9 + - - +
714B ARG* 3.8 17.5 - - - +
715B ASN 3.3 0.2 - - - -
716B MET* 1.3 77.6 - - - +
718B GLN* 1.3 57.4 + - - +
720B GLN* 4.2 4.0 + - - +
721B MET* 3.1 24.6 + - - +
922B GLY 3.2 21.1 - - - +
924B LYS* 3.4 26.2 + - + +
957B ARG* 3.5 27.0 + - - -
10R C 4.2 17.5 + - - -
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Residues in contact with GLN 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700B LEU* 4.6 13.3 - - - +
701B ALA* 5.6 0.5 - - - -
704B THR* 3.7 11.6 + - - -
714B ARG 2.9 18.5 + - - +
715B ASN* 4.1 4.8 - - - +
717B TYR* 1.3 75.2 - - - +
719B CYS* 1.3 64.5 + - - +
720B GLN 3.1 2.5 - - - -
721B MET* 2.8 25.2 + - + -
722B GLY* 2.9 32.0 + - - +
919B SER 3.6 11.0 + - - +
920B ARG* 3.2 48.8 + - - +
921B HIS 4.4 0.4 - - - -
922B GLY* 3.6 11.9 - - - +
1034B GLN* 4.3 5.5 + - - +
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Residues in contact with CYS 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B VAL* 4.2 4.5 - - + +
532B HIS* 3.4 35.6 - - - -
533B THR 3.3 38.6 - - - +
700B LEU* 4.8 9.8 - - + +
715B ASN 2.9 19.1 + - - +
716B MET 3.4 7.6 + - - +
718B GLN* 1.3 79.4 + - - +
720B GLN* 1.3 62.6 + - - +
722B GLY* 4.4 0.2 - - - -
723B LYS* 3.1 30.0 + - - +
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Residues in contact with GLN 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534B PRO* 3.2 38.8 - - + +
535B ASP* 3.4 23.3 - - - +
716B MET 3.8 5.8 + - - +
717B TYR 4.5 7.4 - - - +
718B GLN 3.1 0.4 - - - -
719B CYS* 1.3 77.6 - - - +
721B MET* 1.3 65.9 + - - +
723B LYS* 3.3 29.6 + - - +
724B GLN* 3.0 34.1 + - + +
8R U 3.8 16.8 + - - -
9R U 2.9 25.6 + - - +
10R C 6.0 1.6 - - - +
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Residues in contact with MET 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B TYR* 3.1 21.5 - - - +
718B GLN* 2.8 24.0 + - + +
720B GLN* 1.3 73.9 - - - +
722B GLY* 1.3 60.7 + - - +
724B GLN* 2.9 17.9 + - - -
725B THR* 3.2 17.4 + - - +
916B LYS* 5.4 0.7 - - + -
917B PHE 5.6 0.2 - - - -
918B SER* 3.7 30.3 - - - +
919B SER 4.7 0.2 - - - +
922B GLY 5.0 1.1 - - - +
924B LYS* 3.6 38.4 - - + -
1034B GLN* 4.2 5.2 - - - +
1036B LEU* 3.6 35.2 - - + +
1038B HIS* 4.6 11.2 - - + +
10R C 5.1 4.7 - - - -
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Residues in contact with GLY 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ASN* 2.5 32.9 + - - -
494B TYR* 3.6 6.3 - - - +
700B LEU* 3.8 23.6 - - - -
718B GLN* 2.9 25.8 + - - +
719B CYS 4.4 0.2 - - - -
721B MET* 1.3 74.3 - - - +
723B LYS* 1.3 48.9 + - - +
724B GLN 3.2 0.7 + - - -
725B THR* 3.5 11.9 + - - -
1034B GLN* 4.0 5.6 + - - -
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Residues in contact with LYS 723 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B ASN* 4.2 0.7 - - - +
494B TYR* 5.0 2.7 - - - +
495B ARG* 3.1 50.8 + - + +
498B SER* 3.8 17.0 - - - +
499B HIS* 5.6 6.9 + - + +
502B MET* 5.5 5.6 - - - +
532B HIS* 3.5 35.6 + - + +
534B PRO* 4.7 4.2 - - - +
542B LEU* 4.3 19.8 - - - +
700B LEU* 4.4 2.6 - - + +
719B CYS* 3.1 17.1 + - - +
720B GLN* 3.3 34.6 + - - +
721B MET 3.1 0.8 - - - -
722B GLY* 1.3 74.6 - - - +
724B GLN* 1.3 57.8 + - - +
725B THR 3.8 0.2 - - - -
8R U 5.3 6.9 + - - -
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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
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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