Contacts of the helix formed by residues 705 - 716 (chain N) in PDB entry 5L4K
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 LYS 705 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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666N LYS* 6.0 3.6 - - + -
669N ILE* 3.7 34.8 - - + -
670N ASN* 3.2 27.3 + - - +
673N GLU* 4.3 11.4 - - - +
703N CYS* 2.9 7.1 + - - +
704N PRO* 1.3 96.4 - - + +
706N VAL* 1.3 56.4 + - - +
707N ASN 3.3 0.9 - - - -
708N GLN* 2.9 32.5 + - - +
709N PHE* 2.9 34.2 + - + -
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Residues in contact with VAL 706 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669N ILE* 5.6 0.7 - - + -
695N MET* 3.4 49.8 - - + -
699N THR* 3.9 29.8 - - - +
700N GLU* 4.2 6.7 - - + +
703N CYS* 3.5 13.7 - - + +
704N PRO 3.0 3.6 + - - +
705N LYS* 1.3 77.5 - - - +
707N ASN* 1.3 69.3 + - - +
709N PHE* 4.6 4.9 - - - +
710N ARG* 3.2 29.3 + - - +
737N LEU* 5.7 2.5 - - + +
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Residues in contact with ASN 707 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699N THR* 5.7 0.3 + - - -
700N GLU* 2.6 33.1 + - - +
704N PRO 3.6 8.5 + - - +
705N LYS 3.3 0.2 - - - -
706N VAL* 1.3 85.5 - - - +
708N GLN* 1.3 62.6 + - - +
709N PHE 3.5 0.2 - - - -
710N ARG* 4.0 5.6 - - - -
711N GLN* 3.3 22.7 + - - +
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Residues in contact with GLN 708 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673N GLU* 2.8 33.3 + - - +
704N PRO 4.4 1.7 + - - +
705N LYS* 2.9 40.2 + - - +
707N ASN* 1.3 78.1 - - - +
709N PHE* 1.3 63.5 + - + +
711N GLN* 3.7 8.2 + - - +
712N LEU* 3.4 19.4 + - - +
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Residues in contact with PHE 709 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669N ILE* 3.5 28.0 - - + -
672N LEU* 4.5 5.2 - - + -
673N GLU* 3.7 48.0 - - + -
676N THR* 3.8 22.0 - - - -
687N ALA 5.0 0.4 - - - -
688N LEU* 5.1 1.8 - - + -
691N SER* 3.4 34.1 - - - +
705N LYS* 2.9 30.9 + - + +
706N VAL* 4.8 3.8 - - - +
708N GLN* 1.3 76.6 - - - +
710N ARG* 1.3 59.9 + - - +
712N LEU* 2.9 16.5 + - + +
713N TYR* 2.8 48.9 + + + +
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Residues in contact with ARG 710 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352N ILE* 4.7 11.9 - - - +
706N VAL 3.2 21.9 + - - +
707N ASN* 4.4 5.8 - - - +
708N GLN 3.5 0.2 - - - -
709N PHE* 1.3 73.9 - - - +
711N GLN* 1.3 68.0 + - - +
713N TYR* 2.9 24.5 + - + +
714N SER* 3.3 12.5 + - - +
734N GLN* 5.3 9.6 + - + +
737N LEU* 3.2 31.9 - - + +
738N ASP* 2.6 40.4 + - - -
742N HIS* 5.0 0.2 - - - -
814N PRO* 4.7 18.6 - - - +
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Residues in contact with GLN 711 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707N ASN 3.3 19.4 + - - +
708N GLN* 3.7 7.4 + - - +
710N ARG* 1.3 75.5 - - - +
712N LEU* 1.3 61.4 + - - +
714N SER* 2.9 12.0 + - - -
715N LYS* 2.8 60.8 + - - +
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Residues in contact with LEU 712 (chain N).
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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673N GLU* 5.8 6.1 - - + +
676N THR* 3.6 30.7 - - + -
677N ASN* 5.3 4.9 - - - +
688N LEU* 4.5 9.9 - - + +
708N GLN 3.4 11.9 + - - +
709N PHE* 2.9 24.0 + - + +
711N GLN* 1.3 84.6 - - - +
713N TYR* 1.3 62.8 + - + +
714N SER 3.2 0.4 + - - -
715N LYS* 3.6 25.1 + - + -
716N VAL* 3.5 25.3 - - + +
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Residues in contact with TYR 713 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688N LEU* 3.6 26.9 - - + -
691N SER* 3.0 14.0 + - - -
692N ALA* 3.0 29.2 + - + -
695N MET* 5.9 0.7 - - - +
709N PHE* 2.8 42.9 + + + +
710N ARG* 2.9 16.1 + - + +
712N LEU* 1.3 75.3 - - - +
714N SER* 1.3 57.6 + - - +
716N VAL* 4.0 8.4 - - - +
717N ILE* 3.3 23.0 - - - +
730N ALA* 4.0 4.5 - - - +
733N ALA* 3.0 51.4 - - + -
734N GLN* 3.4 25.8 + - + -
737N LEU* 4.2 15.7 - - + -
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Residues in contact with SER 714 (chain N).
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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710N ARG* 3.3 6.6 + - - +
711N GLN* 2.9 11.2 + - - -
713N TYR* 1.3 73.5 - - - +
715N LYS* 1.3 65.5 + - - +
716N VAL 3.1 3.2 + - - -
717N ILE* 3.1 11.3 + - - +
718N ASN* 2.8 33.9 + - - +
734N GLN* 3.4 25.2 + - - +
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Residues in contact with LYS 715 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711N GLN* 2.8 38.6 + - - +
712N LEU* 3.7 28.3 - - + +
714N SER* 1.3 77.9 - - - +
716N VAL* 1.3 54.3 + - + +
718N ASN* 4.0 7.9 + - - +
719N ASP* 2.6 52.8 + - - +
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Residues in contact with VAL 716 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684N ARG* 5.9 1.8 - - - +
688N LEU* 4.1 11.2 - - + -
712N LEU* 3.5 25.8 - - + +
713N TYR 4.0 1.8 - - - +
715N LYS* 1.3 84.2 - - + +
717N ILE* 1.3 61.9 + - - +
719N ASP* 3.8 9.2 - - - +
722N ASP* 3.8 29.8 - - + +
726N ALA* 6.2 1.3 - - + -
727N LYS* 3.5 27.5 + - - +
730N ALA* 3.4 27.6 - - + -
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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