Contacts of the helix formed by residues 744 - 753 (chain A) in PDB entry 3B7B
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 SER 744 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740A GLN* 4.3 14.6 - - - +
742A LYS 3.4 0.6 + - - -
743A ARG* 1.3 79.1 + - - +
745A PRO* 1.3 76.0 - - - +
746A LEU* 3.3 18.5 + - - +
747A HIS* 3.0 39.1 + - - +
748A ALA* 3.5 4.5 + - - +
770A THR* 4.1 11.7 + - - -
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Residues in contact with PRO 745 (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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1A HIS* 4.7 18.6 - - + +
734A ASN* 6.0 1.6 - - - +
744A SER* 1.3 89.0 - - - +
746A LEU* 1.3 55.3 + - - +
748A ALA* 3.1 10.7 + - + +
749A ALA* 2.8 29.3 + - - +
761A LEU* 4.0 21.2 - - + +
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Residues in contact with LEU 746 (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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744A SER* 3.3 11.2 + - - +
745A PRO* 1.3 80.9 - - - +
747A HIS* 1.3 52.9 + - - +
749A ALA* 4.4 0.4 - - + -
750A ALA* 2.7 33.7 + - - +
758A CYS* 4.0 37.7 - - + +
761A LEU* 4.0 11.9 - - + +
762A VAL* 4.8 4.3 - - + -
766A ALA* 4.5 19.3 - - + -
767A ASN 3.9 8.3 - - - +
768A ILE* 3.7 38.6 - - + +
770A THR* 5.4 0.2 - - - +
778A PRO* 3.8 22.7 - - + -
794A LEU* 4.5 5.4 - - + -
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Residues in contact with HIS 747 (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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742A LYS 4.6 0.4 - - - -
743A ARG* 3.7 23.5 - - + +
744A SER* 3.0 45.3 + - - +
746A LEU* 1.3 75.6 - - - +
748A ALA* 1.3 60.6 + - - +
750A ALA* 3.2 6.5 + - - +
751A GLU* 2.8 33.1 + - - +
770A THR* 3.3 26.2 + - - -
771A CYS 4.2 1.3 - - - -
772A SER* 3.8 14.6 + - - -
776A ARG 2.7 28.8 + - - -
777A THR 3.9 1.8 - - - -
778A PRO* 3.8 21.2 - - + +
781A GLU* 3.7 19.7 - - - +
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Residues in contact with ALA 748 (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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743A ARG* 3.4 26.8 - - - +
744A SER 3.5 3.6 + - - +
745A PRO* 3.1 13.1 + - + +
747A HIS* 1.3 78.7 - - - +
749A ALA* 1.3 62.4 + - - +
751A GLU* 3.4 3.3 + - - +
752A ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 749 (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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745A PRO 2.8 15.2 + - - +
746A LEU 3.7 4.7 - - - +
748A ALA* 1.3 75.8 - - - +
750A ALA* 1.3 63.1 + - - +
752A ALA* 3.1 5.9 + - - +
753A GLY 3.1 16.5 + - - -
754A HIS* 3.2 15.0 + - - +
757A ILE* 3.9 30.7 - - + -
758A CYS* 3.8 19.2 - - - +
761A LEU* 4.3 4.9 - - + -
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Residues in contact with ALA 750 (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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746A LEU 2.7 22.2 + - - +
747A HIS 3.4 4.5 - - - +
749A ALA* 1.3 72.6 - - - +
751A GLU* 1.3 55.9 + - - +
753A GLY* 2.8 25.2 + - - -
758A CYS* 3.7 11.2 - - - -
778A PRO* 3.3 36.8 - - + +
781A GLU* 4.1 0.9 - - + -
782A ALA* 3.7 13.9 - - + +
787A HIS* 3.5 5.7 - - - -
790A ALA* 5.2 0.9 - - - -
794A LEU* 4.2 9.4 - - + -
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Residues in contact with GLU 751 (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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743A ARG* 3.1 24.0 + - - -
747A HIS 2.8 19.6 + - - +
748A ALA 3.7 4.9 - - - +
750A ALA* 1.3 72.6 - - - +
752A ALA* 1.3 57.2 + - + +
753A GLY 3.3 0.2 - - - -
781A GLU* 3.4 30.8 - - + +
785A ASN* 3.5 25.9 + - - +
787A HIS* 2.9 17.3 + - - -
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Residues in contact with ALA 752 (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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748A ALA 3.1 16.1 + - - +
749A ALA* 3.6 6.7 - - - +
750A ALA 3.1 0.4 - - - -
751A GLU* 1.3 75.7 - - - +
753A GLY* 1.3 62.3 + - - +
754A HIS* 3.3 10.4 + - + +
787A HIS* 3.3 14.6 + - - -
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Residues in contact with GLY 753 (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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8A SO4 4.1 8.9 + - - -
749A ALA 3.1 0.8 + - - -
750A ALA 2.8 13.8 + - - -
752A ALA* 1.3 79.4 - - - +
754A HIS* 1.3 59.0 + - - +
755A VAL* 3.0 19.3 + - - +
787A HIS* 3.2 30.8 - - - -
790A ALA* 3.9 8.9 + - - +
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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
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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