Contacts of the helix formed by residues 711 - 720 (chain A) in PDB entry 4MS0
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 ILE 711 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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703A MET* 5.1 2.8 - - + +
710A PRO* 1.3 77.4 - - - +
712A PRO* 1.4 74.1 - - + +
713A MET* 4.0 23.3 - - + +
714A MET* 3.0 48.2 + - + +
715A ASP* 3.4 7.6 + - - +
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Residues in contact with PRO 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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710A PRO 3.8 2.4 - - - +
711A ILE* 1.4 87.4 - - + +
713A MET* 1.3 62.7 + - - +
715A ASP* 3.0 21.3 + - + +
718A LYS* 3.8 38.0 - - + +
721A GLU* 3.3 28.7 - - + +
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Residues in contact with MET 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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693A TYR* 3.6 44.4 - - + +
696A PHE* 3.7 34.8 - - + +
697A TRP* 3.7 6.4 + - - -
711A ILE* 3.2 22.1 + - + +
712A PRO* 1.3 79.3 - - - +
714A MET* 1.3 60.3 + - + +
715A ASP 3.4 0.8 + - - -
722A VAL* 6.3 0.4 - - - -
725A GLY* 4.9 15.3 - - - +
729A PHE* 5.3 5.8 - - + -
900A 2ZX 3.7 19.1 - - + -
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Residues in contact with MET 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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571A SER* 3.8 12.8 - - - +
573A SER* 5.4 5.2 - - - -
696A PHE* 3.6 42.0 - - + +
697A TRP* 3.4 16.9 - - - +
699A GLU* 3.3 45.3 - - - +
700A GLY* 3.3 26.7 - - - -
701A ASP* 5.2 0.2 - - - +
703A MET* 4.4 11.2 - - - +
710A PRO* 4.0 4.7 - - + -
711A ILE* 3.0 34.9 + - + +
713A MET* 1.3 81.0 - - + +
715A ASP* 1.3 58.3 + - - +
716A ARG 3.6 0.9 + - - -
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Residues in contact with ASP 715 (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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697A TRP* 3.7 7.8 + - - -
704A LYS* 2.8 33.1 + - - +
709A GLN* 3.4 20.6 - - - +
710A PRO* 4.0 8.3 - - + +
711A ILE 3.7 9.2 - - - +
712A PRO 3.0 15.4 + - - +
713A MET 3.4 0.4 - - - -
714A MET* 1.3 77.5 - - - +
716A ARG* 1.3 57.9 + - - +
717A ASP* 3.1 13.4 + - - +
718A LYS* 2.9 50.2 + - + +
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Residues in contact with ARG 716 (chain A).
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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694A ALA* 4.9 2.2 + - - +
697A TRP* 3.5 59.7 - - + +
698A ALA* 3.7 8.3 - - - +
701A ASP* 2.7 42.2 + - - +
704A LYS* 4.9 2.8 - - - +
714A MET 3.6 2.4 + - - -
715A ASP* 1.3 73.9 + - - +
717A ASP* 1.3 69.6 + - - +
718A LYS 3.2 1.3 - - - -
719A LYS* 3.2 35.5 - - - +
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Residues in contact with ASP 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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704A LYS* 3.3 20.2 + - - -
715A ASP* 3.1 9.8 + - - +
716A ARG* 1.3 88.2 - - - +
718A LYS* 1.3 63.5 - - + +
719A LYS* 3.5 2.2 + - - -
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Residues in contact with LYS 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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697A TRP* 5.8 0.2 - - - -
709A GLN* 4.2 12.5 + - - +
710A PRO 5.5 1.6 + - - -
712A PRO* 3.8 41.6 - - + +
715A ASP* 2.9 37.6 + - + +
717A ASP* 1.3 82.6 - - - +
719A LYS* 1.3 64.1 + - - +
720A ASP* 3.2 3.8 - - - -
721A GLU* 3.1 43.0 + - - +
722A VAL* 4.1 3.7 + - - +
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Residues in contact with LYS 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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697A TRP* 3.6 47.2 - - + -
715A ASP 4.1 0.6 + - - -
716A ARG* 3.2 31.9 - - - +
717A ASP 3.5 2.2 - - - -
718A LYS* 1.3 75.7 - - - +
720A ASP* 1.3 65.8 + - - +
721A GLU 3.0 1.7 + - - -
722A VAL* 3.2 26.2 + - + +
723A PRO* 4.0 3.3 - - - +
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Residues in contact with ASP 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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718A LYS* 3.2 2.3 - - - -
719A LYS* 1.3 80.3 - - - +
721A GLU* 1.3 63.4 + - + +
722A VAL 3.4 0.4 - - - -
723A PRO* 3.6 12.8 - - - +
724A GLN* 5.3 1.0 + - - +
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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