Contacts of the helix formed by residues 694 - 704 (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 THR 694 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653A THR* 2.7 30.9 + - - +
654A SER* 3.4 18.8 - - - +
692A LEU* 3.0 16.4 + - + +
693A ARG* 1.3 74.0 - - - +
695A LEU* 1.3 64.6 + - - +
696A ASN* 3.1 12.0 + - - +
697A VAL* 3.1 17.7 + - - +
698A LEU* 2.8 20.5 + - - +
821C SEP 4.0 26.9 - - - +
822C ASP 3.5 12.3 - - - +
824C PHE* 4.7 0.2 - - - -
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Residues in contact with LEU 695 (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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678A ASP* 4.3 9.0 - - - +
694A THR* 1.3 76.4 - - - +
696A ASN* 1.3 101.9 + - - +
698A LEU* 3.5 8.7 + - - +
699A LEU* 3.1 47.5 + - + +
770A PRO* 6.1 2.9 - - + -
771A PRO* 6.6 0.4 - - + -
774A LYS* 4.5 23.3 - - + +
778A LEU* 5.9 0.4 - - - +
821C SEP 5.3 9.2 - - - +
822C ASP 4.2 7.6 + - - +
824C PHE* 4.3 17.0 - - + -
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Residues in contact with ASN 696 (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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651A VAL* 4.0 11.6 - - + +
652A MET 4.5 1.0 + - - -
653A THR* 4.0 11.7 - - + -
677A PRO 3.9 7.3 + - - -
678A ASP* 3.4 19.7 + - - +
679A VAL* 3.0 45.7 + - + +
686A VAL* 4.1 6.6 - - + +
694A THR* 3.1 8.3 + - - +
695A LEU* 1.3 100.1 - - - +
697A VAL* 1.3 59.3 + - - +
699A LEU* 4.1 2.1 - - - +
700A GLY* 3.3 18.7 + - - -
821C SEP 3.2 22.4 + - - -
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Residues in contact with VAL 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A THR* 3.7 26.0 - - + -
686A VAL* 4.6 8.3 - - + -
688A SER* 4.9 6.1 - - - -
692A LEU 3.6 19.3 - - - +
693A ARG* 4.8 2.9 - - + -
694A THR* 3.1 10.4 + - - +
696A ASN* 1.3 76.7 - - - +
698A LEU* 1.3 67.5 + - - +
699A LEU 3.3 0.2 - - - -
700A GLY* 3.5 1.5 + - - -
701A ILE* 3.1 35.2 + - + +
707A VAL* 4.7 14.2 - - + +
734A PHE* 3.7 36.8 - - + -
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Residues in contact with LEU 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A ARG* 3.4 43.3 - - + +
694A THR 2.8 34.4 + - - +
695A LEU* 3.7 9.6 - - - +
697A VAL* 1.3 78.5 - - - +
699A LEU* 1.3 62.3 + - - +
701A ILE* 3.1 13.2 + - + +
702A ALA* 3.1 19.2 + - - +
778A LEU* 3.8 19.7 - - + +
817A LEU* 4.0 29.8 - - + +
820A ILE* 4.3 12.5 - - + +
821A THR* 4.0 10.5 - - - +
824C PHE* 4.6 11.9 - - + -
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Residues in contact with LEU 699 (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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678A ASP* 6.1 0.2 - - + -
679A VAL* 3.6 34.5 - - + +
695A LEU* 3.1 32.6 + - + +
696A ASN* 4.3 0.7 - - - +
698A LEU* 1.3 79.6 - - - +
700A GLY* 1.3 63.3 + - - +
702A ALA* 3.0 14.9 + - + +
703A ARG* 3.1 20.2 + - - +
774A LYS* 4.0 37.7 - - + +
777A GLU* 4.3 22.7 - - + +
778A LEU* 3.4 28.9 - - + +
781A LEU* 5.6 2.2 - - + -
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Residues in contact with GLY 700 (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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679A VAL* 4.1 3.1 - - - +
686A VAL* 4.4 9.0 - - - -
696A ASN 3.3 16.1 + - - -
697A VAL 3.5 2.2 + - - -
698A LEU 3.2 0.6 - - - -
699A LEU* 1.3 78.2 - - - +
701A ILE* 1.3 56.0 + - - +
703A ARG 3.2 1.2 + - - -
704A GLY 3.0 23.4 + - - -
705A CYS* 3.0 32.3 + - - +
707A VAL* 4.7 8.1 - - - -
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Residues in contact with ILE 701 (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 VAL* 3.1 35.3 + - + +
698A LEU* 3.4 19.1 - - + +
700A GLY* 1.3 76.5 - - - +
702A ALA* 1.3 61.7 + - - +
703A ARG 3.5 0.3 + - - -
704A GLY* 3.5 1.0 + - - +
705A CYS 5.7 0.4 - - - -
707A VAL* 4.9 4.7 - - + -
734A PHE* 4.3 20.0 - - + -
736A ALA* 4.0 12.6 - - + -
737A ALA* 4.3 22.4 - - + +
740A CYS* 3.2 34.4 - - - +
820A ILE* 3.6 29.2 - - + +
821A THR* 4.8 9.2 - - - +
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Residues in contact with ALA 702 (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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698A LEU 3.1 10.1 + - - +
699A LEU* 3.0 15.1 + - + +
701A ILE* 1.3 81.1 - - - +
703A ARG* 1.3 58.3 + - - +
740A CYS* 5.5 0.4 - - - -
751A TYR* 3.7 14.2 + - - -
753A GLY* 4.8 1.9 + - - -
778A LEU* 4.4 9.4 - - + +
781A LEU* 3.8 39.2 - - + +
782A CYS* 4.1 21.4 - - - -
820A ILE* 5.4 1.1 - - + -
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Residues in contact with ARG 703 (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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679A VAL* 3.9 16.7 + - - +
680A CYS* 3.3 35.4 + - - +
681A GLU* 3.7 33.6 + - - +
683A THR 5.0 1.8 - - - -
699A LEU* 3.1 14.7 + - - +
700A GLY 3.2 0.2 + - - -
702A ALA* 1.3 79.9 - - + +
704A GLY* 1.3 61.4 + - - +
705A CYS* 3.4 21.3 + - - -
744A CYS* 3.7 9.2 - - - -
751A TYR* 3.6 18.9 - - - -
777A GLU* 3.3 24.9 + - - -
781A LEU* 4.1 28.5 - - + +
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Residues in contact with GLY 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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700A GLY 3.0 4.6 + - - -
701A ILE* 3.5 2.8 + - - -
702A ALA 3.4 3.0 + - - -
703A ARG* 1.3 78.6 - - - +
705A CYS* 1.3 67.1 + - - +
737A ALA 5.4 0.4 - - - -
740A CYS* 3.3 34.3 - - - +
741A ARG* 3.2 21.7 - - - +
744A CYS* 4.1 5.0 - - - +
745A HIS* 4.0 9.9 + - - -
751A TYR* 4.0 1.1 - - - -
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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