Contacts of the helix formed by residues 437 - 448 (chain B) in PDB entry 5EEQ
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 437 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436B ILE* 1.3 78.6 - - - +
438B ARG* 1.3 56.9 + - - +
439B GLU* 2.9 27.0 + - - +
440B GLU* 3.1 24.1 + - - +
441B SER* 2.9 29.5 + - - -
458B ARG* 3.8 2.9 - - - +
461B GLN* 3.5 20.4 - - - -
601B PO4 5.1 0.4 - - - -
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Residues in contact with ARG 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B SER* 1.3 74.4 - - - +
439B GLU* 1.3 71.9 + - - +
441B SER* 2.6 19.9 + - - -
442B GLN* 3.1 15.2 + - - +
458B ARG* 3.5 18.7 - - - +
461B GLN* 4.8 0.8 + - - -
462B ARG* 5.4 1.8 - - - +
479B HIS* 3.4 43.5 - - + +
601B PO4 3.0 40.5 + - - +
4M GLY 2.9 29.4 + - - -
5M TYR* 3.1 23.0 - - - +
6M ASP* 5.3 2.2 + - - -
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Residues in contact with GLU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B SER* 2.9 34.5 - - - +
438B ARG* 1.3 88.4 + - - +
440B GLU* 1.3 54.1 + - - +
442B GLN* 3.2 13.5 + - - +
443B ARG* 3.0 27.6 + - - +
461B GLN* 4.1 7.8 + - - +
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Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ILE* 4.0 20.9 - - + -
437B SER* 3.1 27.0 + - - +
439B GLU* 1.3 74.8 - - - +
441B SER* 1.3 63.9 + - - +
443B ARG* 2.8 42.4 + - - +
444B LEU* 2.9 45.3 + - + +
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Residues in contact with SER 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ILE* 4.0 9.4 - - - +
437B SER 2.9 13.5 + - - -
438B ARG 2.6 20.9 + - - -
440B GLU* 1.3 76.4 - - - +
442B GLN* 1.3 56.4 + - - +
444B LEU* 3.4 1.4 + - - +
445B ILE* 2.9 36.0 + - - +
456B LEU* 4.0 15.4 - - - +
458B ARG* 3.7 20.9 + - - -
470B SER* 3.6 8.8 + - - -
479B HIS* 3.3 20.4 - - - -
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Residues in contact with GLN 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B ARG* 3.1 21.1 + - - +
439B GLU* 3.5 12.4 - - - +
440B GLU 3.2 0.2 - - - -
441B SER* 1.3 79.4 + - - +
443B ARG* 1.3 59.7 + - - +
445B ILE* 3.9 0.9 - - - +
446B GLY* 3.0 24.9 + - - -
450B LEU* 5.4 0.5 - - - +
477B VAL* 3.9 33.2 - - + +
479B HIS* 2.8 31.1 + - + +
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Residues in contact with ARG 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B GLU 3.0 12.9 + - - +
440B GLU* 2.8 42.3 + - - +
442B GLN* 1.3 76.6 - - - +
444B LEU* 1.3 62.7 + - - +
446B GLY* 3.2 3.0 + - - -
447B GLN* 2.9 57.4 + - - +
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B HIS* 3.7 31.4 - - + +
436B ILE* 3.8 22.0 - - + -
440B GLU* 2.9 35.9 + - + +
441B SER 3.7 4.0 - - - +
443B ARG* 1.3 79.4 - - - +
445B ILE* 1.3 64.5 + - - +
447B GLN* 3.0 29.5 + - + +
448B GLN* 3.3 15.2 + - - +
456B LEU* 4.3 2.9 - - + -
527B CYS* 4.0 12.1 - - - -
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B SER 2.9 21.4 + - - +
442B GLN 4.0 2.7 - - - +
444B LEU* 1.3 75.3 - - - +
446B GLY* 1.3 61.7 + - - +
448B GLN 3.3 9.0 + - - -
449B GLY 3.5 0.3 + - - -
450B LEU* 3.3 19.4 + - + -
454B LEU* 3.6 21.6 - - + +
456B LEU* 4.2 8.1 - - + +
470B SER* 3.8 30.7 - - - +
471B LEU 4.4 0.7 - - - +
472B CYS* 3.7 27.1 - - + +
477B VAL* 3.8 33.7 - - + -
527B CYS* 4.1 20.2 - - + -
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Residues in contact with GLY 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B GLN 3.0 16.2 + - - -
443B ARG* 3.5 5.4 - - - -
444B LEU 3.2 0.2 - - - -
445B ILE* 1.3 76.9 - - - +
447B GLN* 1.3 63.3 + - - +
449B GLY* 3.2 12.6 + - - -
450B LEU* 4.1 18.0 - - - +
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Residues in contact with GLN 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B ARG* 2.9 57.2 + - - +
444B LEU* 3.0 22.4 + - + +
446B GLY* 1.3 79.7 - - - +
448B GLN* 1.3 62.3 + - + +
449B GLY* 3.3 3.6 + - - -
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Residues in contact with GLN 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B HIS* 5.7 0.2 + - - -
444B LEU* 3.7 13.8 + - - +
445B ILE 3.3 3.7 + - - +
446B GLY 3.2 0.4 - - - -
447B GLN* 1.3 79.4 - - + +
449B GLY* 1.3 59.6 + - - +
450B LEU 3.6 3.2 + - - -
451B VAL* 3.8 11.8 - - - +
454B LEU* 3.7 24.7 - - + +
526B CYS 3.6 7.4 - - - +
527B CYS* 3.3 51.6 + - - +
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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