Contacts of the helix formed by residues 717 - 729 (chain B) in PDB entry 4EG8
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 717 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575B ASP* 3.0 47.3 - - + +
579B TYR* 3.8 18.6 - - + -
606B LEU* 4.1 15.9 - - + -
610B LEU* 3.9 27.6 - - + -
713B LEU* 2.8 25.6 + - + +
714B SER 3.4 3.6 - - - -
716B ILE* 1.3 84.3 - - + +
718B PRO* 1.3 63.0 - - - +
720B LYS* 4.2 7.6 - - + -
721B SER* 2.9 25.3 + - - +
724B ILE* 5.8 1.3 - - + -
762B PHE* 4.1 10.5 - - + -
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Residues in contact with PRO 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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271B ARG* 3.3 44.0 - - - +
323B ASP* 5.0 1.6 - - - +
575B ASP* 3.8 10.8 - - - +
578B LYS* 4.2 15.5 - - + +
714B SER 3.1 15.3 - - - +
715B PRO 3.8 4.5 - - - +
716B ILE 3.2 14.6 - - - +
717B LEU* 1.3 86.4 - - - +
719B ARG* 1.3 65.8 + - + +
721B SER* 3.0 13.9 + - - +
722B VAL* 3.5 14.6 - - - +
804B GOL 3.6 9.5 + - - +
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Residues in contact with ARG 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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323B ASP* 2.7 43.9 + - - +
574B TYR* 6.4 1.3 - - + -
575B ASP* 2.9 22.3 + - - +
718B PRO* 1.3 75.4 - - + +
720B LYS* 1.3 66.5 + - + +
722B VAL* 3.1 22.1 + - - +
723B VAL* 3.3 14.9 + - - +
807B GOL 3.5 47.6 + - - -
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Residues in contact with LYS 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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573B GLY* 6.4 2.0 - - - -
575B ASP* 2.8 28.9 + - + +
717B LEU* 4.2 7.9 - - + -
719B ARG* 1.3 75.6 - - + +
721B SER* 1.3 56.7 + - - +
723B VAL* 3.2 16.0 + - + +
724B ILE* 3.0 33.6 + - + +
760B VAL 5.2 1.2 + - - -
761B LEU* 3.1 36.3 + - + +
762B PHE* 3.7 38.1 - - + -
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Residues in contact with SER 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B THR* 3.9 19.9 - - - +
713B LEU* 5.2 0.7 - - - -
714B SER* 3.5 32.1 - - - -
717B LEU* 2.9 18.2 + - - +
718B PRO 3.0 16.8 + - - -
720B LYS* 1.3 73.1 - - - +
722B VAL* 1.3 65.0 + - - +
724B ILE* 3.3 4.8 + - - +
725B PHE* 2.8 39.1 + - - -
804B GOL 4.1 2.9 + - - -
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Residues in contact with VAL 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B PRO 3.5 16.2 - - - +
719B ARG* 3.1 14.5 + - - +
721B SER* 1.3 84.8 + - - +
723B VAL* 1.3 59.0 + - + +
725B PHE* 3.3 5.1 + - + +
726B ASP* 2.8 42.3 + - - +
732B GLU* 5.6 2.5 - - - +
735B ARG* 3.9 18.8 - - - +
804B GOL 4.8 8.7 - - - +
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Residues in contact with VAL 723 (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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719B ARG 3.3 11.6 + - - +
720B LYS* 3.2 20.9 + - + +
722B VAL* 1.3 79.3 - - + +
724B ILE* 1.3 62.2 + - - +
726B ASP* 3.2 10.5 + - + +
727B MET* 3.0 37.3 + - + +
759B GLU* 5.1 2.0 - - - +
761B LEU* 3.4 24.9 - - + -
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Residues in contact with ILE 724 (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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610B LEU* 4.1 20.6 - - + -
614B VAL* 4.1 15.7 - - + -
706B VAL* 4.1 16.8 - - + -
710B THR* 3.5 35.0 - - + +
717B LEU* 5.8 1.6 - - + -
720B LYS* 3.0 22.6 + - + +
721B SER* 3.6 7.0 - - - +
723B VAL* 1.3 74.9 - - - +
725B PHE* 1.3 64.7 + - + +
727B MET* 3.0 18.7 + - - +
728B LEU* 3.0 19.5 + - + +
761B LEU* 3.4 34.8 - - + -
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Residues in contact with PHE 725 (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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707B ARG* 3.8 30.5 - - + -
710B THR* 3.7 14.8 - - + -
711B LEU* 3.6 37.9 - - + -
714B SER* 4.9 3.8 - - - -
721B SER* 2.8 31.4 + - - +
722B VAL* 3.7 4.0 - - + +
724B ILE* 1.3 78.9 - - + +
726B ASP* 1.3 61.2 + - - +
728B LEU* 3.4 3.4 + - + +
729B GLY 3.0 17.8 + - - -
730B VAL* 3.1 32.3 + - + -
734B HIS 5.2 0.7 - - - -
735B ARG* 3.3 58.6 + - + +
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Residues in contact with ASP 726 (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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722B VAL* 2.8 32.1 + - - +
723B VAL* 3.5 11.4 - - - +
725B PHE* 1.3 71.2 - - - +
727B MET* 1.3 63.5 + - + +
729B GLY* 3.2 10.1 + - - -
735B ARG* 2.9 29.3 + - - +
753B GLY* 3.4 15.9 - - - -
754B PRO* 5.2 0.3 - - - +
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Residues in contact with MET 727 (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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614B VAL* 3.8 23.1 - - - -
615B MET* 4.8 12.8 - - - +
618B THR* 4.2 18.4 - - + +
723B VAL* 3.0 37.6 + - + +
724B ILE* 3.0 6.5 + - - +
726B ASP* 1.3 76.1 - - + +
728B LEU* 1.3 61.6 + - + +
729B GLY 3.1 0.2 - - - -
752B LEU* 3.4 10.6 - - - +
753B GLY* 3.0 26.7 + - - +
754B PRO 5.6 3.8 - - - +
755B ALA* 6.4 0.4 - - - -
759B GLU* 3.2 43.1 - - + +
760B VAL 5.4 0.4 - - - -
761B LEU* 3.6 18.8 - - + +
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Residues in contact with LEU 728 (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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614B VAL* 4.5 3.4 - - + -
617B CYS* 4.2 10.5 - - - -
618B THR* 3.3 25.6 - - + -
628B TRP* 2.8 35.8 + - + -
703B LEU* 3.9 30.3 - - + +
706B VAL* 3.8 25.1 - - + -
707B ARG* 4.1 13.0 - - + +
724B ILE* 3.0 28.8 + - + +
725B PHE* 4.0 2.7 - - + +
727B MET* 1.3 79.1 - - + +
729B GLY* 1.3 59.5 + - - +
730B VAL* 4.0 14.4 - - + -
752B LEU* 3.6 15.1 - - - +
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Residues in contact with GLY 729 (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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725B PHE 3.0 6.4 + - - -
726B ASP* 3.2 8.9 + - - -
727B MET 3.1 5.3 + - - -
728B LEU* 1.3 79.7 - - - +
730B VAL* 1.3 64.5 + - - +
731B PRO* 3.3 3.3 - - - +
735B ARG* 5.0 1.1 - - - -
750B THR* 3.3 21.2 - - - +
751B ARG 3.5 15.9 - - - +
753B GLY* 3.9 5.6 - - - -
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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