Contacts of the helix formed by residues 530 - 539 (chain A) in PDB entry 3V4R
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 530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526A GLY 3.5 3.2 + - - -
527A PHE* 2.7 29.2 + - - -
529A ARG* 1.4 79.8 - - - +
531A GLU* 1.4 67.0 + - - +
532A ARG* 4.1 5.1 + - - +
533A SER* 3.3 15.1 + - - -
534A LEU* 2.9 21.1 + - - +
559A SER* 4.0 7.2 - - - -
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Residues in contact with GLU 531 (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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530A SER* 1.4 70.2 - - - +
532A ARG* 1.4 87.2 + - + +
534A LEU* 3.4 4.1 + - - +
535A ILE* 3.0 37.3 + - + +
559A SER* 3.6 36.6 + - - +
562A ILE* 3.7 41.3 - - + +
563A ALA* 4.2 0.8 - - - +
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Residues in contact with ARG 532 (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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341A HIS* 4.3 19.3 - - + -
395A THR* 3.6 35.3 + - - +
396A PRO 3.0 27.9 + - - -
397A GLY* 3.6 3.8 - - - -
398A PRO* 3.4 36.7 - - - +
401A ILE* 3.6 10.7 - - - +
530A SER* 3.3 5.2 + - - +
531A GLU* 1.4 101.3 + - + +
533A SER* 1.3 64.3 + - - +
535A ILE* 3.3 3.6 + - + +
536A GLN* 3.1 29.3 + - - +
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Residues in contact with SER 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A LEU* 3.9 15.4 - - - +
527A PHE* 2.9 38.6 + - - -
528A LEU* 3.6 25.2 - - - +
530A SER* 3.2 15.2 + - - -
532A ARG* 1.3 75.7 - - - +
534A LEU* 1.3 54.4 + - - +
536A GLN* 3.2 5.0 + - - +
537A THR* 2.7 37.1 + - - -
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Residues in contact with LEU 534 (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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519A ILE* 4.1 34.5 - - + -
522A ALA 4.7 3.4 - - - +
528A LEU 4.2 5.8 - - - +
529A ARG* 3.6 32.3 - - - +
530A SER 2.9 15.8 + - - +
531A GLU 3.6 4.0 - - - +
533A SER* 1.3 75.7 - - - +
535A ILE* 1.3 56.3 + - - +
537A THR* 3.1 6.9 + - - +
538A ILE* 2.8 39.0 + - + +
551A MET* 4.7 7.0 - - + -
559A SER 4.1 5.6 - - - +
560A MET* 3.9 41.3 - - + +
563A ALA* 3.9 10.5 - - + -
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Residues in contact with ILE 535 (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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394A ALA* 5.6 2.0 - - + -
395A THR* 3.4 34.1 - - + -
531A GLU* 3.0 23.5 + - + +
532A ARG* 3.3 1.5 + - + +
534A LEU* 1.3 74.8 - - - +
536A GLN* 1.3 61.8 + - - +
538A ILE* 3.5 9.7 + - + +
539A GLY* 3.1 19.2 + - - -
562A ILE* 4.7 8.3 - - + -
563A ALA* 3.8 30.1 - - + +
566A GLU* 4.2 20.4 - - + -
567A THR* 5.2 6.1 - - - +
570A ARG* 4.5 18.4 - - - +
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Residues in contact with GLN 536 (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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41A THR* 5.1 10.3 - - - +
339A GLU* 3.7 18.4 + - - +
341A HIS* 4.1 18.7 - - - +
394A ALA* 3.4 25.3 + - - +
395A THR* 3.4 20.6 + - + +
505A LEU* 3.7 21.5 - - + +
532A ARG 3.1 15.7 + - - +
533A SER* 3.6 9.0 - - - +
535A ILE* 1.3 77.1 - - - +
537A THR* 1.4 59.3 + - - +
539A GLY* 3.4 13.7 + - - -
540A ARG* 3.7 21.7 + - - +
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Residues in contact with THR 537 (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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451A THR* 4.1 14.7 - - + +
504A LEU* 4.2 10.5 - - + +
505A LEU* 3.5 16.0 - - - +
517A VAL* 3.9 17.4 - - + +
519A ILE* 3.9 29.8 - - + -
528A LEU* 4.7 6.6 + - - +
529A ARG* 6.3 0.4 - - - +
533A SER 2.7 22.3 + - - -
534A LEU* 3.1 11.1 + - + +
536A GLN* 1.4 70.9 - - - +
538A ILE* 1.4 65.8 + - - +
540A ARG* 3.2 23.8 + - - +
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Residues in contact with ILE 538 (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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419A ASP* 5.3 2.2 - - - +
420A PRO* 3.4 35.3 - - + +
422A ILE* 3.8 15.0 - - + -
519A ILE* 4.5 2.7 - - + -
534A LEU 2.8 28.2 + - - +
535A ILE* 3.6 8.1 - - + +
536A GLN 3.4 0.2 - - - -
537A THR* 1.4 73.2 - - - +
539A GLY* 1.3 58.7 + - - +
540A ARG 3.0 5.9 + - - -
541A ALA* 3.1 14.2 + - - +
549A VAL* 3.9 28.7 - - + -
551A MET* 3.8 22.9 - - + -
563A ALA* 4.0 13.9 - - + -
567A THR* 4.0 24.0 - - + +
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Residues in contact with GLY 539 (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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41A THR* 4.5 10.9 + - - -
413A ARG* 6.0 0.7 - - - -
419A ASP* 4.9 5.8 - - - -
510A ASP* 3.3 19.8 - - - +
535A ILE 3.1 13.9 + - - -
536A GLN* 3.7 7.9 - - - -
537A THR 3.2 1.4 - - - -
538A ILE* 1.3 75.2 - - - +
540A ARG* 1.3 59.0 + - - +
541A ALA 3.1 1.8 + - - -
542A ALA* 3.3 23.2 + - - +
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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