Contacts of the helix formed by residues 434 - 446 (chain A) in PDB entry 3D7T
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 LEU 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A GLU* 3.2 23.8 - - + +
306A GLU* 3.8 7.6 + - - +
432A SER* 2.7 10.9 + - - +
433A PHE* 1.3 78.6 - - - +
435A GLN* 1.3 70.6 + - + +
436A LEU 3.1 1.5 + - - -
437A ARG* 3.3 5.2 + - - +
438A GLU* 3.0 49.7 + - + +
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Residues in contact with GLN 435 (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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431A PRO* 3.5 25.9 - - + +
432A SER* 3.0 18.0 + - - +
434A LEU* 1.3 82.4 - - + +
436A LEU* 1.3 56.5 + - - +
438A GLU* 3.2 11.9 - - + +
439A GLN* 3.0 40.4 + - - +
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Residues in contact with LEU 436 (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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299A CYS* 3.4 13.7 - - - -
369A VAL* 4.2 10.3 - - + -
372A PHE* 4.0 19.1 - - + -
418A VAL* 3.8 29.2 - - + +
422A CYS* 3.8 11.4 - - - -
431A PRO* 3.8 24.7 - - + -
432A SER 2.8 19.4 + - - +
433A PHE* 3.7 29.4 - - + -
435A GLN* 1.3 72.6 - - - +
437A ARG* 1.3 56.0 + - - +
438A GLU 3.0 1.6 - - - -
439A GLN* 2.9 13.9 + - - +
440A LEU* 2.7 37.8 + - + +
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Residues in contact with ARG 437 (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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245A HIS* 5.6 4.8 + - - -
296A LEU* 4.0 13.2 - - + -
299A CYS* 3.2 17.3 - - - -
300A GLU* 2.7 50.4 + - + +
303A GLU* 3.1 33.7 + - - +
433A PHE 4.0 0.2 - - - +
434A LEU 3.3 5.8 + - - +
436A LEU* 1.3 78.0 - - - +
438A GLU* 1.3 56.3 + - - +
440A LEU* 3.8 6.0 - - - +
441A GLU* 2.9 43.2 + - + +
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Residues in contact with GLU 438 (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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434A LEU* 3.0 42.3 + - + +
435A GLN* 3.2 15.0 - - + +
436A LEU 3.0 0.4 - - - -
437A ARG* 1.3 78.6 - - - +
439A GLN* 1.3 57.8 + - + +
441A GLU* 3.8 4.0 - - - +
442A HIS* 2.9 29.4 + - - +
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Residues in contact with GLN 439 (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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418A VAL* 4.0 25.1 - - + +
421A ASN* 3.3 30.1 + - - +
431A PRO* 4.5 2.4 - - - +
435A GLN* 3.0 31.6 + - - +
436A LEU* 2.9 16.5 + - - +
438A GLU* 1.3 74.1 - - + +
440A LEU* 1.3 61.3 + - - +
442A HIS* 3.5 9.0 - - + +
443A ILE* 3.0 35.6 + - + +
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Residues in contact with LEU 440 (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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292A LEU* 4.5 14.7 - - + +
295A SER* 3.9 20.6 - - - +
296A LEU* 3.5 36.6 - - + -
299A CYS* 3.9 24.2 - - + -
372A PHE* 4.9 6.1 - - + -
376A LEU* 5.4 4.9 - - + -
415A VAL* 6.1 3.1 - - + -
418A VAL* 4.2 30.5 - - + -
436A LEU* 2.7 24.1 + - + +
437A ARG* 3.8 1.6 - - - +
439A GLN* 1.3 71.4 - - - +
441A GLU* 1.3 54.9 + - - +
443A ILE* 3.4 10.2 - - + +
444A LYS* 2.7 35.3 + - - +
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Residues in contact with GLU 441 (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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296A LEU* 3.9 12.5 - - - +
300A GLU* 5.1 1.6 - - - +
437A ARG* 2.9 37.2 + - + +
438A GLU* 3.8 3.6 - - - +
440A LEU* 1.3 73.6 - - - +
442A HIS* 1.3 60.6 + - - +
444A LYS* 3.0 36.4 + - - +
445A THR* 2.5 48.9 + - - +
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Residues in contact with HIS 442 (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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438A GLU 2.9 18.4 + - - +
439A GLN* 3.5 11.4 - - - +
441A GLU* 1.3 72.9 - - - +
443A ILE* 1.3 58.1 + - + +
445A THR* 4.8 0.7 - - - -
446A HIS* 2.7 79.0 + + - +
448A LEU* 4.5 13.9 - - + +
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Residues in contact with ILE 443 (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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292A LEU* 4.4 9.6 - - + -
414A ALA* 3.4 44.2 - - + +
415A VAL* 4.0 9.0 - - + +
418A VAL* 4.0 15.5 - - + -
439A GLN* 3.0 19.7 + - + +
440A LEU* 3.4 10.8 - - + +
442A HIS* 1.3 82.3 - - + +
444A LYS* 1.3 63.0 + - - +
446A HIS 3.3 0.3 - - - -
447A GLU 3.1 3.8 + - - -
448A LEU* 2.6 63.9 + - + +
449A HIS* 4.2 10.1 - - + +
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Residues in contact with LYS 444 (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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292A LEU* 3.4 26.2 - - + -
293A LYS* 4.7 18.0 - - - +
296A LEU* 3.7 18.6 - - + +
440A LEU 2.7 21.6 + - - +
441A GLU* 3.2 26.0 + - - +
443A ILE* 1.3 73.7 - - - +
445A THR* 1.3 60.9 + - - +
447A GLU* 2.8 28.9 + - - +
449A HIS* 3.7 8.7 - - + +
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Residues in contact with THR 445 (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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441A GLU* 2.5 37.4 + - - +
442A HIS* 4.0 1.6 - - - -
444A LYS* 1.3 78.2 - - - +
446A HIS* 1.3 70.0 + - + +
447A GLU* 3.0 12.0 + - - +
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Residues in contact with HIS 446 (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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442A HIS* 2.7 66.2 + + - +
443A ILE 3.3 0.7 - - - -
445A THR* 1.3 82.5 - - + +
447A GLU* 1.3 66.7 + - - +
448A LEU* 3.0 25.0 + - + +
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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