Contacts of the helix formed by residues 436 - 447 (chain D) in PDB entry 5CDP
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 GLY 436 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434D VAL* 3.6 2.7 - - - +
435D GLU* 1.3 79.5 - - - +
437D ASP* 1.4 61.2 + - - -
438D SER* 3.2 4.9 + - - -
439D ALA* 3.4 5.3 + - - +
440D GLY 3.0 20.6 + - - -
456D PRO* 3.6 14.2 - - - +
457D LEU 3.6 9.9 - - - -
458D ARG* 5.6 0.2 - - - -
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Residues in contact with ASP 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 4.2 2.6 + - - -
436D GLY* 1.4 71.2 - - - -
438D SER* 1.3 64.0 + - - +
439D ALA 3.3 0.2 - - - -
440D GLY* 4.1 2.9 - - - +
441D GLY* 3.1 20.6 + - - -
444D LYS* 4.7 7.9 + - - -
456D PRO* 3.6 23.0 - - - +
457D LEU 4.9 0.2 + - - -
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Residues in contact with SER 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 3.0 28.3 + - - +
118A ALA 5.6 0.4 - - - -
119A ALA* 3.6 20.7 - - - +
120A ALA* 3.3 23.9 + - - +
123A PHE* 3.7 22.9 - - - -
436D GLY* 3.2 1.9 - - - -
437D ASP* 1.3 77.4 - - - +
439D ALA* 1.3 58.9 + - - +
442D SER* 4.2 2.6 + - - -
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Residues in contact with ALA 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D VAL* 4.1 18.8 - - + -
435D GLU* 4.7 4.9 - - + +
436D GLY 3.4 13.4 + - - +
437D ASP 3.3 0.2 - - - -
438D SER* 1.3 76.6 - - - +
440D GLY* 1.3 58.2 + - - +
442D SER* 3.4 7.3 + - - -
443D THR* 2.7 37.2 + - - +
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Residues in contact with GLY 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D VAL* 3.8 13.4 - - - +
436D GLY 3.0 15.6 + - - -
437D ASP* 3.3 7.1 + - - -
439D ALA* 1.3 76.0 - - - +
441D GLY* 1.3 51.5 + - - +
443D THR* 3.3 3.9 + - - -
444D LYS* 2.8 46.8 + - - +
454D ILE* 4.3 5.5 - - - +
456D PRO* 4.6 7.2 - - - -
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Residues in contact with GLY 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN* 3.8 19.0 - - - +
116A ASP* 4.9 18.0 - - - +
117A GLY 5.4 0.2 - - - -
437D ASP 3.1 11.6 + - - -
439D ALA 3.4 0.2 - - - -
440D GLY* 1.3 69.8 - - - +
442D SER* 1.4 64.5 + - - +
444D LYS* 3.4 11.8 + - - +
445D SER* 3.1 26.3 + - - -
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Residues in contact with SER 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLY 4.9 0.5 - - - -
109A ASN* 3.3 35.4 + - - +
438D SER 4.3 1.9 + - - -
439D ALA* 3.4 13.8 + - - -
441D GLY* 1.4 71.7 - - - +
443D THR* 1.4 55.2 + - - +
445D SER* 3.3 6.8 + - - -
446D GLY* 2.9 32.1 + - - -
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Residues in contact with THR 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D PHE* 4.6 13.9 - - + -
434D VAL* 3.7 18.5 - - + +
439D ALA* 2.7 24.6 + - - +
440D GLY 3.5 4.5 - - - -
442D SER* 1.4 74.7 - - - +
444D LYS* 1.4 55.2 + - - +
446D GLY* 5.2 0.7 - - - -
447D ARG* 3.0 36.1 + - + +
454D ILE* 3.4 30.7 - - + -
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Residues in contact with LYS 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASP* 4.6 24.2 + - - +
417D LYS 4.5 5.8 + - - -
419D ALA* 3.7 27.1 - - + +
437D ASP* 4.7 7.5 + - - -
440D GLY 2.8 29.3 + - - +
441D GLY* 3.4 7.5 + - - +
443D THR* 1.4 72.2 - - - +
445D SER* 1.3 58.6 + - - +
447D ARG* 3.2 29.2 + - - +
449D SER* 5.7 0.2 - - - -
454D ILE* 3.5 22.9 - - + -
456D PRO* 4.3 22.6 - - - +
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Residues in contact with SER 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLY 5.2 1.2 + - - -
112A SER* 3.8 24.1 - - - -
116A ASP* 5.4 0.5 + - - -
297A SER* 5.0 2.8 - - - -
298A LEU* 3.6 32.7 + - - +
441D GLY 3.1 16.0 + - - -
442D SER* 3.7 4.9 - - - -
444D LYS* 1.3 78.8 - - - +
446D GLY* 1.3 59.8 + - - +
447D ARG 3.7 4.3 + - - +
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Residues in contact with GLY 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LEU* 4.2 16.1 - - - +
299A ARG* 2.8 25.1 + - - -
442D SER 2.9 16.2 + - - -
443D THR* 4.1 1.1 - - - -
445D SER* 1.3 74.4 - - - +
447D ARG* 1.3 61.2 + - - +
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Residues in contact with ARG 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A THR 5.3 1.0 - - - +
297A SER* 4.7 8.5 - - - -
299A ARG* 3.7 9.9 + - - -
419D ALA* 3.0 32.7 + - - +
420D ASP 3.1 16.4 + - - -
432D PHE* 6.3 0.4 - - + -
443D THR* 3.0 16.6 + - + +
444D LYS* 3.2 28.3 + - - +
445D SER 3.5 4.7 - - - +
446D GLY* 1.3 79.6 - - - +
448D ASP* 1.3 59.0 + - - +
449D SER* 3.8 27.2 + - - +
452D GLN* 2.8 54.4 + - + +
454D ILE* 3.2 24.3 - - + +
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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