Contacts of the helix formed by residues 640 - 649 (chain A) in PDB entry 1ZXE
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 640 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630A ILE* 4.1 28.7 - - + -
636A LYS 4.2 3.4 - - - +
637A LEU* 2.9 22.8 + - + +
639A THR* 1.3 96.1 - - - +
641A LEU* 1.3 60.7 + - - +
642A SER 3.4 2.5 - - - -
643A GLU* 3.5 10.0 + - - +
644A VAL* 3.0 29.1 + - + +
784A LEU* 3.9 25.4 - - + -
856A LEU* 4.5 29.8 - - + +
857A ALA* 5.0 6.1 - - - +
858A LYS* 5.7 4.5 - - + +
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Residues in contact with LEU 641 (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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637A LEU* 3.5 17.9 - - + +
638A SER* 3.2 22.7 + - - +
640A ILE* 1.3 75.7 - - - +
642A SER* 1.3 61.6 + - - +
644A VAL* 3.2 6.3 + - + +
645A MSE 2.9 33.8 + - + +
663A LEU* 5.5 4.7 - - + -
784A LEU* 3.8 28.5 - - + -
641B LEU* 3.9 18.6 - - + -
642B SER* 3.6 39.5 - - - +
645B MSE 3.7 24.7 - - + -
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Residues in contact with SER 642 (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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638A SER 4.3 4.4 + - - -
639A THR 5.5 3.4 - - - -
640A ILE 3.4 0.4 - - - -
641A LEU* 1.3 78.3 - - - +
643A GLU* 1.3 66.9 + - - +
645A MSE 3.2 4.8 + - - +
646A LEU* 2.9 35.9 + - - +
858A LYS* 6.2 0.9 - - - -
634B GLU* 5.1 6.8 + - - +
638B SER* 5.1 8.7 - - - -
641B LEU* 3.6 19.3 - - - +
663B LEU* 4.1 7.8 - - - +
768B ARG* 5.5 0.9 + - - -
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Residues in contact with GLU 643 (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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639A THR 4.9 0.7 - - - +
640A ILE* 3.5 12.4 + - - +
641A LEU 3.3 0.4 - - - -
642A SER* 1.3 77.4 - - - +
644A VAL* 1.3 58.8 + - + +
646A LEU* 3.0 11.5 + - - +
647A LEU* 2.9 32.8 + - + +
834A ARG* 3.1 29.7 + - - -
856A LEU* 2.6 36.0 - - + +
858A LYS* 2.8 41.4 + - - +
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Residues in contact with VAL 644 (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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640A ILE* 3.0 27.0 + - + +
641A LEU* 3.2 8.5 + - + +
643A GLU* 1.3 75.5 - - - +
645A MSE 1.3 58.1 + - - +
647A LEU* 3.3 9.8 + - - +
648A ALA* 2.9 28.9 + - + +
658A TYR* 5.5 5.0 - - + +
661A ALA* 3.9 22.0 - - + -
784A LEU* 4.5 6.5 - - + -
786A ILE* 3.8 37.0 - - + -
856A LEU* 4.2 17.9 - - + -
645B MSE 5.3 1.6 - - + -
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Residues in contact with MSE 645 (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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641A LEU 2.9 25.0 + - - +
642A SER 3.5 6.5 - - - +
644A VAL* 1.3 78.7 - - - +
646A LEU* 1.3 62.5 + - - +
648A ALA* 3.3 12.2 + - - +
649A SER 3.3 6.4 + - - -
661A ALA* 6.2 0.7 - - - -
641B LEU* 3.8 27.8 - - + +
644B VAL* 5.4 1.6 - - + -
645B MSE 4.3 21.5 - - - +
661B ALA* 3.0 23.3 - - + +
662B TRP* 2.9 37.5 - - - +
663B LEU* 3.0 32.5 + - + +
784B LEU* 3.1 27.6 - - + -
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Residues in contact with LEU 646 (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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642A SER* 2.9 28.8 + - - +
643A GLU* 3.2 13.0 - - - +
645A MSE 1.3 76.8 - - - +
647A LEU* 1.3 59.7 + - - +
649A SER* 2.8 26.8 + - - +
650A LEU* 4.0 1.2 - - - +
829A GLN* 4.2 10.5 - - + +
831A ILE* 3.7 24.0 - - + +
634B GLU* 4.7 0.2 - - - +
663B LEU* 3.6 35.9 - - + +
768B ARG* 3.7 55.0 - - + +
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Residues in contact with LEU 647 (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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643A GLU* 2.9 17.3 + - + +
644A VAL* 3.7 8.7 - - - +
646A LEU* 1.3 74.0 - - - +
648A ALA* 1.3 65.8 + - - +
650A LEU* 3.1 29.1 + - + +
658A TYR* 4.0 31.6 + - + +
831A ILE* 3.8 20.9 - - + -
854A PHE* 3.3 53.6 - - + -
856A LEU* 3.5 32.8 - - + -
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Residues in contact with ALA 648 (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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644A VAL* 2.9 16.1 + - + +
645A MSE 3.4 11.7 - - - +
646A LEU 3.2 0.2 - - - -
647A LEU* 1.3 77.5 - - - +
649A SER* 1.3 61.1 + - - +
650A LEU 3.3 1.2 + - - -
657A ARG* 3.8 4.5 + - - -
658A TYR* 3.4 22.9 - - + +
659A TYR 4.9 2.5 - - - +
660A ALA* 5.8 2.5 - - - -
661A ALA* 6.6 0.2 - - + -
594B ARG* 3.1 27.6 + - - +
661B ALA 3.7 11.2 - - - +
662B TRP* 3.5 15.5 - - + -
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Residues in contact with SER 649 (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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645A MSE 3.3 2.0 + - - -
646A LEU* 2.8 16.8 + - - +
647A LEU 3.1 1.2 - - - -
648A ALA* 1.3 77.8 - - - +
650A LEU* 1.3 60.5 + - - +
829A GLN* 5.3 0.7 + - - +
593B LEU* 3.6 21.0 - - - +
594B ARG* 3.1 25.9 + - - -
662B TRP* 3.7 21.7 - - - +
663B LEU 2.9 27.7 + - - -
664B GLU* 3.8 9.2 - - - +
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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