Contacts of the helix formed by residues 703 - 722 (chain B) in PDB entry 5N4D
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 703 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B SER* 3.3 16.6 - - - +
696B LEU* 6.1 0.4 - - + -
701B GLY 4.6 1.3 - - - +
702B LYS* 1.4 89.3 - - + +
704B THR* 1.3 66.4 + - - +
705B ASP* 3.4 20.0 - - - +
706B LYS* 3.1 12.6 + - + +
707B ASN* 3.0 18.9 + - - -
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Residues in contact with THR 704 (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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79B ARG* 4.3 22.8 + - - +
103B LEU* 3.2 51.6 + - + +
104B GLN 3.2 15.4 + - - -
105B SER* 3.0 13.9 + - - -
702B LYS 3.6 1.8 + - - -
703B PRO* 1.3 71.1 - - - +
705B ASP* 1.3 65.3 + - - +
707B ASN* 3.1 12.2 + - + +
708B VAL* 2.8 27.1 + - + +
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Residues in contact with ASP 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 6.2 2.5 - - - +
703B PRO* 3.4 18.5 - - - +
704B THR* 1.3 79.6 - - - +
706B LYS* 1.3 73.8 + - - +
708B VAL* 3.4 8.0 + - - +
709B LYS* 3.1 26.5 + - - +
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Residues in contact with LYS 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B LYS* 5.5 0.4 - - - +
692B ASP* 3.0 32.8 + - - +
702B LYS* 3.7 19.1 - - + +
703B PRO* 3.1 20.5 + - + +
705B ASP* 1.3 83.9 + - - +
707B ASN* 1.3 60.6 + - - +
709B LYS* 3.2 16.2 + - + +
710B ASP* 2.8 54.6 + - - +
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Residues in contact with ASN 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 5.5 12.6 - - - +
701B GLY* 5.7 0.8 - - - -
702B LYS* 3.3 45.1 + - - +
703B PRO 3.0 11.5 + - - -
704B THR* 3.4 13.0 + - + +
706B LYS* 1.3 76.8 - - - +
708B VAL* 1.3 58.5 + - + +
710B ASP* 3.3 5.7 + - - +
711B ALA* 2.8 30.9 + - - +
12D GLU 4.9 12.4 + - - +
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Residues in contact with VAL 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 3.8 29.2 - - + +
75B PHE* 4.4 6.3 - - + +
76B ARG* 3.9 36.3 - - + +
79B ARG* 3.9 28.0 - - + -
103B LEU* 5.3 1.1 - - + -
510B ILE* 5.1 1.3 - - + -
704B THR* 2.8 27.4 + - + +
705B ASP* 3.7 10.3 - - - +
707B ASN* 1.3 71.7 - - + +
709B LYS* 1.3 65.6 + - - +
711B ALA* 3.2 7.2 + - - +
712B ALA* 2.9 21.8 + - - +
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Residues in contact with LYS 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 3.0 29.4 + - - +
68B ILE* 6.4 0.7 - - + -
72B ALA* 5.2 4.9 - - + -
690B LYS* 4.6 3.8 - - - +
705B ASP 3.1 15.3 + - - +
706B LYS* 3.7 18.6 - - + +
708B VAL* 1.3 78.0 - - - +
710B ASP* 1.3 72.1 + - - +
712B ALA* 3.2 7.6 + - + +
713B ASP* 2.7 52.5 + - - +
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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
----------------------------------------------------------
690B LYS* 3.0 29.4 + - - +
702B LYS* 2.6 39.7 + - - +
706B LYS* 2.8 39.9 + - - +
707B ASN* 3.8 6.2 - - - +
709B LYS* 1.3 80.8 - - - +
711B ALA* 1.3 61.7 + - - +
713B ASP* 3.3 2.9 + - - +
714B LYS* 3.0 25.4 + - - +
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Residues in contact with ALA 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 3.8 8.3 - - + -
510B ILE* 3.9 27.6 - - + -
707B ASN 2.8 16.8 + - - +
708B VAL 3.7 4.0 - - - +
710B ASP* 1.3 77.4 - - - +
712B ALA* 1.4 61.6 + - - +
714B LYS* 3.2 8.5 + - - +
715B TRP* 2.9 41.0 + - + +
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Residues in contact with ALA 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 3.6 21.3 - - + +
71B LEU* 4.1 3.4 - - + +
72B ALA* 3.5 37.9 - - + +
75B PHE* 3.8 10.9 - - + -
708B VAL 2.9 13.3 + - - +
709B LYS* 3.2 8.0 + - + +
711B ALA* 1.4 75.4 - - - +
713B ASP* 1.3 57.8 + - - +
716B GLY* 2.9 28.4 + - - -
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Residues in contact with ASP 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 4.9 1.4 + - - -
62B LEU* 3.9 26.8 - - + +
68B ILE* 3.4 25.7 - - - +
654B LEU* 4.7 3.1 - - + -
690B LYS* 3.1 23.9 + - - +
709B LYS* 2.7 48.7 + - - +
710B ASP 3.6 8.1 - - - +
711B ALA 3.2 0.2 - - - -
712B ALA* 1.3 77.1 - - - +
714B LYS* 1.3 56.9 + - - +
717B PHE* 2.8 32.1 + - - +
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Residues in contact with LYS 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B ASN* 3.5 25.9 + - - +
599B VAL* 3.8 18.5 - - + +
601B GLU* 2.7 30.4 + - - +
654B LEU* 4.5 12.1 - - + -
656B THR* 5.7 4.3 - - + -
710B ASP 3.0 15.4 + - - +
711B ALA* 3.2 7.4 + - - +
713B ASP* 1.3 77.8 - - - +
715B TRP* 1.3 100.6 + - + +
717B PHE* 3.4 2.9 + - - +
718B ILE* 3.1 27.8 + - + +
13D HIS* 3.8 17.6 + - - -
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Residues in contact with TRP 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 4.0 2.5 - - + -
75B PHE* 3.5 24.7 - + + -
492B ILE* 3.6 38.8 - - + -
494B TYR* 5.8 0.9 - + - -
510B ILE* 3.7 19.8 - - + +
511B ILE* 4.4 22.6 - - + +
514B PHE* 3.5 35.2 - + + -
522B PHE* 5.4 2.2 - + - -
574B ASN* 3.8 18.6 - - + -
711B ALA* 2.9 28.6 + - + +
714B LYS* 1.3 101.4 - - + +
716B GLY* 1.3 62.6 + - - +
718B ILE* 3.3 36.7 + - + +
719B ALA* 2.8 23.9 + - - +
13D HIS* 6.3 0.2 - - - -
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Residues in contact with GLY 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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65B ASN* 3.2 18.1 + - - -
67B ASP* 5.8 1.1 - - - -
68B ILE* 3.9 11.0 - - - -
71B LEU* 3.5 17.1 - - - +
518B TYR* 5.3 0.4 - - - -
712B ALA 2.9 20.0 + - - -
715B TRP* 1.3 73.6 - - - +
717B PHE* 1.3 65.6 + - - +
719B ALA* 3.8 3.9 - - - +
720B ARG 2.9 19.4 + - - -
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Residues in contact with PHE 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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61B TYR* 4.0 20.0 - + - -
62B LEU* 4.2 20.4 - - + -
65B ASN* 4.8 3.1 - - - +
68B ILE* 4.7 1.2 - - - +
597B ALA* 4.9 1.8 - - + -
598B ALA 4.7 1.8 - - - -
599B VAL* 4.5 8.1 - - + -
652B ALA* 3.7 29.8 - - + -
653B THR 3.7 23.3 - - - -
654B LEU* 3.6 38.4 - - + -
686B PRO* 4.2 6.1 - - + -
688B LEU* 4.0 22.4 - - + -
713B ASP 2.8 20.6 + - - +
714B LYS 3.6 4.0 - - - +
716B GLY* 1.3 75.2 - - - +
718B ILE* 1.3 67.1 + - + +
720B ARG* 3.4 2.0 + - - +
721B ALA* 2.9 27.1 + - + +
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Residues in contact with ILE 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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492B ILE* 4.2 14.8 - - + -
514B PHE* 4.5 4.5 - - + -
572B ALA* 3.6 28.7 - - + -
573B ILE 5.2 1.3 - - - +
574B ASN* 5.1 4.0 - - + -
597B ALA* 4.2 16.6 - - + -
599B VAL* 3.7 29.4 - - + -
714B LYS* 3.1 12.4 + - + +
715B TRP* 3.4 42.0 - - + +
716B GLY 3.3 0.2 - - - -
717B PHE* 1.3 77.1 - - + +
719B ALA* 1.3 66.0 + - - +
721B ALA* 3.2 1.7 + - - +
722B LEU* 2.9 35.4 + - + +
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Residues in contact with ALA 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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514B PHE* 4.1 3.6 - - + -
518B TYR* 3.5 42.8 - - + +
715B TRP 2.8 21.3 + - - +
716B GLY* 3.8 4.9 - - - +
718B ILE* 1.3 74.2 - - - +
720B ARG* 1.3 62.8 + - - +
722B LEU 3.2 0.9 + - - -
723B GLY 3.1 4.3 + - - -
724B LEU* 2.9 43.7 + - + +
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Residues in contact with ARG 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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61B TYR* 4.8 24.7 - - + +
64B GLN* 3.1 29.5 + - - +
65B ASN* 3.4 48.5 + - - +
66B ALA* 4.5 3.2 - - - +
67B ASP* 4.6 11.1 + - - -
716B GLY 2.9 9.0 + - - +
717B PHE* 4.0 3.1 - - - +
719B ALA* 1.3 75.8 - - - +
721B ALA* 1.3 65.2 + - - +
723B GLY* 3.0 15.0 + - - +
724B LEU 4.7 5.8 - - - +
725B GLU* 5.5 3.4 + - - -
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Residues in contact with ALA 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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596B GLY 4.0 4.9 - - - +
597B ALA* 3.8 16.4 - - + -
652B ALA* 3.6 31.2 - - + -
717B PHE* 2.9 20.9 + - + +
718B ILE 3.6 4.0 - - - +
720B ARG* 1.3 80.3 - - - +
722B LEU* 1.3 61.5 + - - +
723B GLY 3.6 0.5 + - - -
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Residues in contact with LEU 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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490B ALA* 3.7 16.8 - - + -
491B ALA 4.4 2.2 - - - +
492B ILE* 5.1 0.9 - - + -
569B GLY 3.7 12.3 - - - +
570B LYS* 3.5 46.8 + - + +
572B ALA* 4.1 8.1 - - + +
596B GLY* 3.5 40.2 - - - +
597B ALA* 4.0 3.8 - - + +
718B ILE* 2.9 37.4 + - + +
719B ALA 3.9 3.1 - - - +
720B ARG 3.2 0.4 - - - -
721B ALA* 1.3 76.0 - - - +
723B GLY* 1.3 60.0 + - - +
724B LEU* 3.4 19.6 + - + +
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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
------------------------------------------------------------
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