Contacts of the helix formed by residues 703 - 722 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A SER* 3.3 17.9 - - - +
696A LEU* 6.2 0.2 - - + -
701A GLY 4.6 1.3 - - - +
702A LYS* 1.3 91.2 - - + +
704A THR* 1.3 66.1 + - - +
705A ASP* 3.5 19.1 - - - +
706A LYS* 3.1 13.0 + - + +
707A ASN* 3.0 18.7 + - - -
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Residues in contact with THR 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG* 4.6 17.8 + - - +
102A GLY 5.5 0.4 - - - +
103A LEU* 3.1 53.8 + - + +
104A GLN 3.2 15.6 + - - -
105A SER* 3.0 13.6 + - - -
702A LYS 3.6 1.2 + - - -
703A PRO* 1.3 72.0 - - - +
705A ASP* 1.3 65.3 + - - +
707A ASN* 3.1 12.0 + - + +
708A VAL* 2.9 30.0 + - + +
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Residues in contact with ASP 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 6.1 3.1 - - - +
703A PRO* 3.5 18.1 - - - +
704A THR* 1.3 78.6 - - - +
706A LYS* 1.3 74.5 + - - +
708A VAL* 3.3 8.5 + - - +
709A LYS* 3.0 27.2 + - - +
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Residues in contact with LYS 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LYS* 5.3 1.1 - - - +
692A ASP* 3.0 31.3 + - - +
702A LYS* 3.8 19.3 - - + +
703A PRO* 3.1 20.3 + - + +
705A ASP* 1.3 84.8 + - - +
707A ASN* 1.3 59.9 + - - +
709A LYS* 3.2 18.8 + - + -
710A ASP* 2.9 52.8 + - - +
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Residues in contact with ASN 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 5.1 16.5 - - - +
701A GLY* 5.6 0.6 - - - -
702A LYS* 3.3 44.8 + - - +
703A PRO 3.0 12.4 + - - -
704A THR* 3.1 11.9 + - - +
706A LYS* 1.3 76.6 - - - +
708A VAL* 1.3 59.0 + - + +
710A ASP* 3.4 6.7 + - - +
711A ALA* 2.9 29.8 + - - +
12C GLU 4.9 13.7 + - - +
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Residues in contact with VAL 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 3.7 29.6 - - + +
75A PHE* 4.3 6.9 - - + -
76A ARG* 3.8 37.9 - - + +
79A ARG* 4.7 17.9 - - + +
103A LEU* 5.2 0.7 - - + -
510A ILE* 5.1 3.4 - - + -
704A THR* 2.9 28.8 + - + +
705A ASP* 3.7 10.3 - - - +
707A ASN* 1.3 76.1 - - + +
709A LYS* 1.3 58.3 + - - +
711A ALA* 3.2 7.0 + - - +
712A ALA* 2.9 28.8 + - - +
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Residues in contact with LYS 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLN* 3.2 17.8 + - - -
68A ILE* 6.3 0.2 - - + -
72A ALA* 5.3 4.5 - - + -
690A LYS* 4.2 3.8 - - - +
705A ASP 3.0 14.0 + - - +
706A LYS* 3.2 26.2 + - + +
708A VAL* 1.3 76.7 - - - +
710A ASP* 1.3 59.4 + - - +
712A ALA* 3.3 7.5 + - + +
713A ASP* 2.7 54.2 + - - +
801A GOL 3.2 26.3 + - - -
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Residues in contact with ASP 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LYS* 2.9 29.3 + - - +
702A LYS* 2.8 38.0 + - - +
706A LYS* 2.9 38.3 + - - +
707A ASN* 3.8 7.1 - - - +
709A LYS* 1.3 77.9 - - - +
711A ALA* 1.4 56.9 + - - +
713A ASP* 3.3 3.1 + - - +
714A LYS* 2.9 30.5 + - - +
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Residues in contact with ALA 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 3.8 6.7 - - + -
510A ILE* 3.9 27.4 - - + -
707A ASN 2.9 18.3 + - - +
708A VAL 3.2 4.0 + - - +
710A ASP* 1.4 76.8 - - - +
712A ALA* 1.3 56.7 + - - +
714A LYS* 3.3 8.5 + - - +
715A TRP* 2.9 48.6 + - + +
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Residues in contact with ALA 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 3.5 21.3 - - + +
71A LEU* 4.2 3.5 - - + +
72A ALA* 3.5 36.3 - - + +
75A PHE* 3.7 12.0 - - + -
708A VAL 2.9 17.5 + - - +
709A LYS* 3.7 4.7 - - + +
711A ALA* 1.3 75.7 - - - +
713A ASP* 1.3 59.1 + - - +
716A GLY* 2.8 29.3 + - - -
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Residues in contact with ASP 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.9 20.4 - - + +
68A ILE* 3.4 18.3 - - - +
654A LEU* 4.7 3.1 - - + -
690A LYS* 2.7 26.1 + - - +
709A LYS* 2.7 40.3 + - - +
710A ASP 3.5 7.2 - - - +
712A ALA* 1.3 78.1 - - - +
714A LYS* 1.3 57.8 + - - +
717A PHE* 2.9 32.1 + - - +
801A GOL 2.7 25.3 + - - -
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Residues in contact with LYS 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A ASN* 3.4 20.8 + - - +
599A VAL* 3.8 24.5 - - + +
601A GLU* 2.9 29.8 + - - +
654A LEU* 4.4 12.1 - - + +
656A THR* 5.7 4.5 - - + -
710A ASP 2.9 16.7 + - - +
711A ALA* 3.8 8.1 - - - +
713A ASP* 1.3 77.7 - - - +
715A TRP* 1.3 100.1 + - + +
717A PHE* 3.3 2.6 + - - +
718A ILE* 3.1 27.2 + - + +
13C HIS* 3.8 19.0 + - - -
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Residues in contact with TRP 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 4.0 2.5 - - - -
75A PHE* 3.5 24.0 - + + -
492A ILE* 3.5 41.3 - - + -
494A TYR* 5.7 0.7 - + - -
510A ILE* 3.6 20.3 - - + +
511A ILE* 4.1 26.2 - - + +
514A PHE* 3.4 36.8 - + + -
522A PHE* 5.2 1.3 - + - -
574A ASN* 3.9 17.5 - - + -
711A ALA* 2.9 33.5 + - - +
714A LYS* 1.3 97.6 - - + +
716A GLY* 1.3 60.6 + - - +
718A ILE* 3.4 27.3 + - + +
719A ALA* 2.8 23.6 + - - +
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Residues in contact with GLY 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ASN* 3.2 17.4 + - - -
67A ASP* 5.9 1.1 - - - -
68A ILE* 4.0 10.8 - - - -
71A LEU* 3.6 16.2 - - - +
518A TYR* 5.3 0.2 - - - -
712A ALA 2.8 19.7 + - - -
713A ASP 4.0 0.2 - - - -
715A TRP* 1.3 75.8 - - - +
717A PHE* 1.3 63.4 + - - +
719A ALA* 3.8 4.0 - - - +
720A ARG 2.9 19.9 + - - -
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Residues in contact with PHE 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 3.9 26.5 - + - -
62A LEU* 4.0 22.2 - - + -
65A ASN* 4.8 3.1 - - - +
68A ILE* 4.7 1.2 - - - +
597A ALA* 4.9 1.3 - - + -
598A ALA 4.6 1.6 - - - -
599A VAL* 4.4 9.2 - - + -
652A ALA* 3.7 27.6 - - + -
653A THR 3.7 26.2 - - - -
654A LEU* 3.6 37.0 - - + -
686A PRO* 4.1 9.0 - - + -
688A LEU* 4.1 12.3 - - + -
713A ASP 2.9 19.4 + - - +
714A LYS 3.6 4.0 - - - +
716A GLY* 1.3 74.7 - - - +
718A ILE* 1.3 68.1 + - + +
720A ARG* 3.4 3.7 + - + +
721A ALA* 2.9 27.3 + - + +
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Residues in contact with ILE 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A ILE* 4.0 16.2 - - + -
514A PHE* 4.5 2.5 - - + -
572A ALA* 3.6 29.4 - - + -
573A ILE 5.2 1.1 - - - +
574A ASN* 5.1 5.2 - - + -
597A ALA* 4.2 11.0 - - + -
599A VAL* 3.8 27.6 - - + -
714A LYS* 3.1 13.9 + - + +
715A TRP* 3.5 39.0 - - + +
716A GLY 3.2 0.2 - - - -
717A PHE* 1.3 80.2 - - + +
719A ALA* 1.3 65.4 + - - +
721A ALA* 3.2 5.2 + - - +
722A LEU* 3.0 34.8 + - + +
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Residues in contact with ALA 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A PHE* 4.0 4.9 - - + -
518A TYR* 3.5 42.2 - - + +
715A TRP 2.8 20.5 + - - +
716A GLY* 3.3 6.0 + - - +
718A ILE* 1.3 74.4 - - - +
720A ARG* 1.3 62.1 + - - +
722A LEU 3.3 0.7 + - - -
723A GLY 3.1 3.8 + - - -
724A LEU* 2.8 44.2 + - + +
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Residues in contact with ARG 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 4.4 28.6 + - + +
64A GLN* 3.4 30.1 + - - +
65A ASN* 3.4 49.6 + - - +
66A ALA 4.6 2.8 - - - +
67A ASP* 5.1 6.9 + - - -
716A GLY 2.9 8.0 + - - +
717A PHE* 4.0 3.1 - - - +
719A ALA* 1.3 78.3 - - - +
721A ALA* 1.3 64.2 + - - +
723A GLY* 3.0 14.1 + - - -
724A LEU 4.7 4.9 - - - +
725A GLU* 5.5 4.2 + - - -
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Residues in contact with ALA 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A GLY 4.0 5.9 - - - +
597A ALA* 3.8 16.8 - - + -
652A ALA* 3.6 31.4 - - + -
717A PHE* 2.9 19.7 + - + +
718A ILE 3.2 4.7 + - - +
720A ARG* 1.3 78.9 - - - +
722A LEU* 1.3 61.1 + - - +
723A GLY 3.5 0.3 + - - -
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Residues in contact with LEU 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A ALA* 3.9 12.8 - - + -
491A ALA 4.5 2.5 - - - +
492A ILE* 5.0 1.3 - - + -
569A GLY 3.9 11.2 - - - +
570A LYS* 2.9 61.0 + - + +
572A ALA* 4.0 9.0 - - + -
596A GLY* 3.5 40.6 - - - +
597A ALA* 3.9 3.8 - - + +
718A ILE* 3.0 36.1 + - + +
719A ALA 4.0 2.7 - - - +
721A ALA* 1.3 75.5 - - - +
723A GLY* 1.3 60.6 + - - +
724A LEU* 3.4 14.9 + - + +
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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
------------------------------------------------------------
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