Contacts of the helix formed by residues 735 - 747 (chain B) 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 PRO 735 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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731B SER 3.8 10.7 - - - +
732B HIS 5.0 3.1 - - - +
733B HIS 3.6 10.3 - - - +
734B PHE* 1.3 85.5 - - - +
736B ALA* 1.3 59.4 + - - +
738B PRO* 3.1 21.9 - - + +
739B LEU* 3.3 17.0 - - + +
821B THR* 3.8 26.7 - - + +
822B GLN* 5.4 7.4 - - + -
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Residues in contact with ALA 736 (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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701B ILE* 3.8 15.3 - - + -
734B PHE 3.4 0.4 - - - -
735B PRO* 1.3 78.5 - - - +
737B ALA* 1.3 67.3 + - - +
739B LEU* 2.9 23.4 + - - +
740B CYS* 3.0 13.9 + - - -
820B ILE 3.2 20.2 - - - +
821B THR* 3.2 21.1 + - - +
823B HIS* 3.8 15.0 - - + -
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Residues in contact with ALA 737 (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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701B ILE* 4.3 15.6 - - + +
704B GLY* 5.3 0.7 - - - -
705B CYS 4.7 3.2 - - - +
707B VAL* 4.0 29.4 - - + +
729B GLU* 4.5 5.2 - - + +
730B LEU 5.0 3.8 - - - +
731B SER* 5.2 0.4 - - - -
734B PHE* 3.4 24.6 + - + +
735B PRO 3.3 0.2 - - - -
736B ALA* 1.3 79.7 - - - +
738B PRO* 1.3 70.5 - - + +
740B CYS* 3.2 1.9 + - - +
741B ARG* 3.1 23.1 + - - +
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Residues in contact with PRO 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B GLU* 3.4 26.9 - - - +
731B SER* 3.5 27.6 - - - -
734B PHE 3.0 15.3 - - - +
735B PRO* 3.1 16.4 - - + +
737B ALA* 1.3 93.4 - - + +
739B LEU* 1.3 62.5 + - + +
741B ARG* 4.1 7.1 + - + +
742B SER* 3.3 24.3 + - - -
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Residues in contact with LEU 739 (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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735B PRO* 3.3 24.5 - - + +
736B ALA* 2.9 15.5 + - - +
738B PRO* 1.3 79.7 - - + +
740B CYS* 1.3 62.0 + - - +
742B SER* 4.0 3.7 - - - -
743B GLU* 3.4 22.9 + - - +
823B HIS* 4.0 37.0 + - + +
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Residues in contact with CYS 740 (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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701B ILE* 3.2 38.1 - - + +
702B ALA* 5.3 1.1 - - - -
704B GLY* 3.7 7.2 - - - -
736B ALA 3.0 18.0 + - - +
737B ALA 4.0 2.0 - - - +
739B LEU* 1.3 75.2 - - - +
741B ARG* 1.3 65.8 + - - +
742B SER 3.1 1.8 - - - -
743B GLU* 3.3 3.7 + - - +
744B CYS* 2.9 27.7 + - - +
751B TYR* 3.4 22.1 + - - +
823B HIS* 3.7 25.4 - - - -
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Residues in contact with ARG 741 (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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704B GLY* 3.1 23.9 - - - +
705B CYS 3.8 11.0 - - - +
706B TRP* 3.0 48.4 - - + -
726B GLU* 4.3 18.7 + - - -
729B GLU* 3.4 23.9 + - - +
737B ALA 3.1 16.7 + - - +
738B PRO* 4.2 8.8 + - - +
740B CYS* 1.3 76.8 - - - +
742B SER* 1.3 85.8 + - - +
745B HIS* 3.2 45.9 + - + +
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Residues in contact with SER 742 (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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738B PRO 3.3 18.3 + - - -
739B LEU* 4.0 4.7 - - - -
740B CYS 3.1 0.4 - - - -
741B ARG* 1.3 97.8 + - - +
743B GLU* 1.3 66.5 + - - +
744B CYS 3.0 1.0 + - - -
745B HIS* 3.2 2.3 + - - +
746B LEU* 3.1 36.8 + - - +
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Residues in contact with GLU 743 (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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739B LEU 3.4 16.3 + - - +
740B CYS 3.3 3.3 + - - +
742B SER* 1.3 78.7 - - - +
744B CYS* 1.3 57.1 + - - +
746B LEU* 3.4 18.8 - - + +
747B SER* 3.2 25.1 + - - -
751B TYR* 3.4 29.7 + - + -
752B ARG 5.0 3.3 - - - +
753B GLY* 5.4 0.2 - - - -
754B THR* 4.5 23.3 + - - +
823B HIS* 4.7 12.1 + - - -
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Residues in contact with CYS 744 (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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703B ARG 3.7 11.9 - - - +
704B GLY* 4.4 2.2 - - - -
740B CYS 2.9 18.8 + - - +
741B ARG 3.9 2.9 - - - +
743B GLU* 1.3 76.9 - - - +
745B HIS* 1.3 78.7 + - + +
747B SER* 3.1 19.9 - - - +
751B TYR* 3.4 43.8 - - + +
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Residues in contact with HIS 745 (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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684B THR* 5.8 0.8 + - - -
704B GLY 3.5 13.1 + - - -
705B CYS* 5.1 2.0 - - - -
706B TRP* 3.7 29.3 - + - -
741B ARG* 3.2 48.8 + - + +
742B SER 4.2 1.1 - - - +
744B CYS* 1.3 91.6 - - + +
746B LEU* 1.3 63.4 + - - +
747B SER 3.6 4.0 + - - +
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Residues in contact with LEU 746 (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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742B SER* 3.1 33.5 + - - +
743B GLU* 3.4 22.4 - - + +
745B HIS* 1.3 76.7 - - - +
747B SER* 1.3 75.4 + - - +
748B ALA* 3.3 3.5 + - - +
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Residues in contact with SER 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B GLU 3.2 13.4 + - - -
744B CYS* 3.1 21.2 - - - +
745B HIS 3.2 5.1 - - - +
746B LEU* 1.3 88.7 - - - +
748B ALA* 1.3 64.9 + - - +
749B GLY 2.7 26.3 + - - +
750B PRO 3.5 12.0 + - - -
751B TYR* 4.2 7.6 - - - -
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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
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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