Contacts of the helix formed by residues 700 - 716 (chain B) in PDB entry 3K5N
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 PRO 700 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695B TYR* 4.3 19.1 - - + -
697B ARG* 5.8 2.2 - - + -
698B ASN* 2.8 19.1 - - - +
699B VAL* 1.3 98.7 - - - +
701B PRO* 1.3 73.6 - - + +
702B HIS* 3.4 29.6 - - + +
703B VAL* 3.0 20.3 - - + +
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Residues in contact with PRO 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B VAL 4.2 2.2 - - - +
700B PRO* 1.3 85.3 - - + +
702B HIS* 1.3 63.9 + - - +
704B ARG* 3.0 34.0 - - + +
705B ALA* 3.1 7.3 + - - +
730B TYR* 4.7 8.1 - - + +
732B TRP* 3.3 43.1 - - + -
737B PRO* 3.5 15.7 - - + +
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Residues in contact with HIS 702 (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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686B LYS* 3.0 48.2 - - + +
687B ARG 3.3 15.9 + - - -
688B LEU* 4.3 12.8 - - + +
689B ARG 5.5 0.2 + - - -
695B TYR* 4.6 10.5 + - - -
700B PRO* 3.4 25.1 - - + +
701B PRO* 1.3 78.7 - - - +
703B VAL* 1.3 74.5 + - - +
705B ALA* 3.2 2.9 + - - +
706B ALA* 2.9 21.4 + - - +
728B ILE* 4.2 5.6 - - + +
730B TYR* 3.0 41.1 + - + +
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Residues in contact with VAL 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B LEU* 3.8 20.6 - - + -
692B LEU* 4.6 4.5 - - + -
695B TYR* 3.9 31.9 - - + -
699B VAL* 3.6 14.1 - - + -
700B PRO* 3.0 37.0 + - + +
702B HIS* 1.3 84.0 + - - +
704B ARG* 1.3 69.4 + - - +
706B ALA* 2.7 7.6 - - - +
707B ARG* 2.5 55.0 + - + +
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Residues in contact with ARG 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B VAL* 2.7 53.2 + - + +
701B PRO* 3.0 39.1 - - - +
703B VAL* 1.3 83.5 - - + +
705B ALA* 1.3 55.7 + - - +
706B ALA 2.8 1.3 - - - -
707B ARG* 3.6 10.0 - - + +
708B LEU* 2.5 46.7 + - + +
732B TRP* 4.6 9.5 - - - -
737B PRO* 3.8 22.1 - - + +
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Residues in contact with ALA 705 (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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701B PRO 3.1 13.0 + - - +
702B HIS 3.6 8.1 - - - +
704B ARG* 1.3 76.0 - - - +
706B ALA* 1.3 56.8 + - - +
708B LEU* 3.2 5.7 + - - +
709B ALA* 2.9 27.5 + - - +
728B ILE* 4.7 2.7 - - + -
730B TYR* 3.4 35.2 - - + -
737B PRO 4.4 1.3 + - - -
738B GLU* 3.8 8.3 - - - +
739B PRO* 3.4 27.9 - - + +
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Residues in contact with ALA 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B LEU* 3.9 9.4 - - + -
692B LEU* 4.4 6.4 - - + +
702B HIS 2.9 12.7 + - - +
703B VAL* 2.7 17.0 + - - +
705B ALA* 1.3 76.2 - - - +
707B ARG* 1.3 63.1 + - - +
709B ALA 3.4 0.7 + - - -
710B ASP* 3.3 20.3 + - - +
722B TYR* 3.6 24.0 - - + +
728B ILE* 3.4 27.3 - - + +
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Residues in contact with ARG 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B LEU* 2.5 55.7 + - + +
693B SER* 4.1 5.7 + - - +
695B TYR* 3.4 24.1 + - - +
696B GLN* 4.6 4.6 + - - -
698B ASN 5.4 2.2 + - - -
699B VAL* 5.1 7.7 - - - +
703B VAL* 2.5 37.3 + - - +
704B ARG* 3.6 10.1 - - + +
706B ALA* 1.3 71.4 - - - +
708B LEU* 1.3 71.0 + - + +
709B ALA 3.3 0.2 + - - -
710B ASP* 3.4 10.2 + - - +
711B GLU* 3.5 15.6 + - - +
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Residues in contact with LEU 708 (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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704B ARG* 2.5 31.0 + - + +
705B ALA* 3.2 9.2 - - - +
707B ARG* 1.3 76.5 - - + +
709B ALA* 1.3 60.5 + - - +
711B GLU* 2.8 37.3 - - - +
712B GLU* 3.4 7.7 + - - +
737B PRO 4.3 3.6 - - - +
738B GLU* 4.1 24.2 - - + +
739B PRO* 4.0 17.3 - - + -
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Residues in contact with ALA 709 (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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705B ALA 2.9 12.8 + - - +
706B ALA 3.8 0.7 - - - +
707B ARG 3.2 0.2 - - - -
708B LEU* 1.3 82.7 - - - +
710B ASP* 1.3 51.4 + - - +
712B GLU* 2.9 6.9 + - - +
713B ASN* 2.6 36.8 + - - +
722B TYR* 3.6 26.9 - - + +
739B PRO* 3.7 18.4 - - + -
741B ASP* 5.4 1.1 - - - +
742B TYR* 3.6 18.2 - - + -
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Residues in contact with ASP 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B LEU* 5.7 0.9 - - + -
706B ALA 3.3 10.7 + - - +
707B ARG* 3.4 4.2 + - - +
708B LEU 3.3 0.2 - - - -
709B ALA* 1.3 76.2 - - - +
711B GLU* 1.3 69.5 + - - +
713B ASN* 2.7 30.5 + - - +
714B GLN* 2.7 20.4 + - - +
720B LEU* 2.8 24.6 - - + +
721B GLN 3.1 12.7 + - - -
722B TYR* 3.4 16.8 + - - -
723B GLN* 2.0 40.0 + - - +
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Residues in contact with GLU 711 (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 3.5 12.5 + - - +
708B LEU* 2.8 33.2 - - - +
710B ASP* 1.3 74.1 - - - +
712B GLU* 1.3 61.2 + - + +
714B GLN* 2.4 43.4 + - + +
715B LYS* 2.9 26.1 + - - +
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Residues in contact with GLU 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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708B LEU 3.6 9.4 - - - +
709B ALA* 3.0 13.0 - - - +
711B GLU* 1.3 85.7 - - + +
713B ASN* 1.3 60.6 + - - +
714B GLN 3.1 0.5 + - - -
715B LYS* 3.2 32.0 + - - +
716B ARG* 3.3 45.3 + - - +
742B TYR* 3.9 25.0 - - + +
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Residues in contact with ASN 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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709B ALA 2.6 17.4 + - - -
710B ASP* 2.7 34.3 + - - +
712B GLU* 1.3 73.2 - - - +
714B GLN* 1.3 61.9 + - - +
716B ARG 3.3 2.1 + - - -
717B GLY 3.0 3.6 + - - -
718B ARG* 2.9 45.9 + - - +
719B PRO 3.5 10.8 + - - +
720B LEU* 4.1 2.5 - - + -
721B GLN* 3.5 29.0 + - - +
722B TYR* 4.7 2.2 - - - -
742B TYR* 2.6 34.4 + - - -
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Residues in contact with GLN 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 ASP 2.7 11.3 + - - +
711B GLU* 2.4 31.2 + - + +
713B ASN* 1.3 69.7 - - - +
715B LYS* 1.3 66.9 + - + +
717B GLY* 2.6 26.4 + - - -
718B ARG 4.5 0.7 - - - -
720B LEU* 4.4 18.2 - - + +
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Residues in contact with LYS 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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711B GLU* 2.9 33.0 + - - +
712B GLU* 3.2 29.5 + - - +
714B GLN* 1.3 79.5 - - + +
716B ARG* 1.3 61.5 + - + +
717B GLY* 2.7 10.1 + - - -
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Residues in contact with ARG 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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712B GLU* 3.3 36.8 + - - +
713B ASN* 3.8 5.8 - - - +
714B GLN 3.2 0.4 - - - -
715B LYS* 1.3 76.3 - - + +
717B GLY* 1.3 64.1 - - - +
718B ARG* 3.2 48.2 + - - +
742B TYR* 3.7 24.7 - - - -
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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