Contacts of the helix formed by residues 710 - 720 (chain A) in PDB entry 3T1N
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 TYR 710 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655A MET* 4.1 21.1 - - + -
659A LYS* 3.6 43.8 - - + +
662A VAL* 3.0 36.5 - - + +
663A VAL* 3.8 27.4 - - + -
687A LEU* 5.4 4.5 - - + -
688A SER 3.4 18.0 + - - +
689A GLY* 4.8 6.7 - - - +
709A SER* 1.3 72.3 - - - +
711A ASP* 1.3 61.3 + - - +
712A TRP 3.2 0.4 - - - -
713A VAL* 3.1 24.7 + - + +
714A LEU* 3.4 41.3 + - + +
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Residues in contact with ASP 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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709A SER* 2.8 19.0 + - - +
710A TYR* 1.3 78.5 - - - +
712A TRP* 1.3 62.7 + - - +
713A VAL 3.0 0.2 - - - -
714A LEU* 3.0 34.9 + - - +
715A TRP* 3.0 28.4 + - - -
728A PHE* 3.6 22.4 - - + -
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Residues in contact with TRP 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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650A LEU* 4.7 5.6 - - + -
673A PHE* 4.7 7.0 - + - -
685A HIS* 3.7 23.6 - + - -
687A LEU* 3.7 34.5 - - + -
708A LEU* 3.6 14.1 - - + -
709A SER 3.0 11.6 + - - +
711A ASP* 1.3 77.8 - - - +
713A VAL* 1.3 57.3 + - + +
716A SER* 2.6 39.8 + - - -
722A TRP* 3.6 46.4 - + + -
723A ILE* 3.1 43.4 + - + +
724A SER 3.5 14.8 + - - -
725A GLU* 3.9 19.4 - - + +
728A PHE* 3.8 27.7 - + + -
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Residues in contact with VAL 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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650A LEU* 5.5 0.4 - - + -
662A VAL* 4.6 9.0 - - + -
663A VAL* 4.6 14.8 - - + -
666A VAL* 4.0 28.0 - - + +
687A LEU* 3.6 32.3 - - + -
710A TYR* 3.1 28.5 + - + +
711A ASP 3.0 0.4 - - - -
712A TRP* 1.3 88.0 - - + +
714A LEU* 1.3 68.3 + - - +
715A TRP 3.2 0.2 - - - -
716A SER* 3.1 6.2 + - - -
717A LEU* 2.8 22.9 + - - +
722A TRP* 4.9 7.6 - - + -
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Residues in contact with LEU 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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662A VAL* 5.1 5.6 - - + -
710A TYR* 3.4 47.3 + - + +
711A ASP* 3.0 26.6 + - - +
713A VAL* 1.3 80.0 - - - +
715A TRP* 1.3 60.7 + - + +
717A LEU* 3.2 13.8 + - + +
718A GLU* 2.9 28.0 + - - +
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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
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711A ASP* 3.0 30.6 + - - +
714A LEU* 1.3 77.7 - - + +
716A SER* 1.3 65.7 + - - +
717A LEU 3.1 2.0 - - - -
718A GLU* 4.1 20.6 - - + -
719A LEU* 3.0 55.8 + - + +
723A ILE* 3.5 22.0 - - + -
728A PHE* 4.0 21.2 - + - -
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Residues in contact with SER 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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666A VAL* 5.1 0.4 - - - -
670A LEU* 3.5 5.7 - - - +
712A TRP* 2.6 29.6 + - - -
713A VAL* 3.1 7.1 + - - -
715A TRP* 1.3 76.0 - - - +
717A LEU* 1.3 56.7 + - - +
720A GLY* 3.0 5.2 + - - -
721A HIS 3.0 40.8 + - - +
722A TRP* 3.7 24.5 - - - -
723A ILE* 3.4 25.4 + - - +
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Residues in contact with LEU 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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662A VAL* 5.2 9.9 - - + -
666A VAL* 3.9 30.3 - - + +
669A LYS* 4.7 22.4 - - + -
670A LEU* 5.1 3.8 - - + -
713A VAL 2.8 12.2 + - - +
714A LEU* 3.4 15.3 - - + +
716A SER* 1.3 75.5 - - - +
718A GLU* 1.3 68.2 + - - +
719A LEU 3.0 3.4 + - - -
720A GLY* 3.1 13.0 + - - -
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Residues in contact with GLU 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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714A LEU 2.9 16.5 + - - +
715A TRP* 3.4 29.6 + - + +
717A LEU* 1.3 78.6 - - - +
719A LEU* 1.3 63.6 + - + +
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Residues in contact with LEU 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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715A TRP* 3.0 49.1 + - + +
716A SER 4.4 0.4 - - - +
718A GLU* 1.3 84.8 - - + +
720A GLY* 1.3 61.4 + - - +
721A HIS* 3.6 27.3 - - + +
723A ILE* 3.5 27.6 - - + -
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Residues in contact with GLY 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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669A LYS* 5.6 5.8 - - - -
670A LEU* 4.0 16.5 - - - +
716A SER 3.0 8.7 + - - -
717A LEU 3.1 10.3 + - - -
719A LEU* 1.3 78.6 - - - +
721A HIS* 1.3 68.2 + - - +
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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