Contacts of the helix formed by residues 516 - 528 (chain B) in PDB entry 1UPX
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 516 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B ASP* 3.8 14.4 - - - -
138B ASP* 2.8 27.1 + - - -
141B SER* 3.0 20.7 + - - -
514B PHE 3.8 0.2 - - - -
515B LEU* 1.3 73.7 - - - +
517B PRO* 1.3 76.4 - - - +
519B VAL* 3.1 18.8 + - - +
520B ALA* 2.8 21.9 + - - +
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Residues in contact with PRO 517 (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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137B ASP* 6.0 2.2 - - + -
515B LEU 4.5 0.9 - - - +
516B SER* 1.3 89.2 - - - +
518B ASN* 1.3 64.4 + - - +
520B ALA* 3.6 5.2 + - + +
521B LYS* 3.0 27.9 + - - +
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Residues in contact with ASN 518 (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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138B ASP* 2.7 35.5 + - - +
516B SER* 3.3 1.8 + - - -
517B PRO* 1.3 83.2 - - - +
519B VAL* 1.3 58.6 + - - +
521B LYS* 3.4 14.7 + - - +
522B VAL* 3.1 31.9 + - + +
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Residues in contact with VAL 519 (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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138B ASP* 3.9 10.8 - - + +
141B SER* 3.6 22.7 - - - +
142B LEU* 3.7 42.6 - - + -
145B LEU* 4.8 2.7 - - + -
188B VAL* 5.6 1.8 - - + -
192B VAL* 6.0 1.1 - - + -
515B LEU* 4.1 18.4 - - + -
516B SER* 3.1 21.7 + - - +
518B ASN* 1.3 75.4 - - - +
520B ALA* 1.3 65.7 + - - +
522B VAL* 3.1 10.8 + - + +
523B LEU* 3.0 29.6 + - + +
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Residues in contact with ALA 520 (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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511B LEU* 6.4 2.5 - - + -
515B LEU* 4.2 21.9 - - + +
516B SER 2.8 18.1 + - - +
517B PRO* 3.8 5.4 - - + +
519B VAL* 1.3 76.4 - - - +
521B LYS* 1.3 63.3 + - - +
523B LEU* 3.2 9.2 + - - +
524B VAL* 3.0 30.8 + - + +
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Residues in contact with LYS 521 (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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517B PRO 3.0 18.8 + - - +
518B ASN* 3.4 15.7 - - - +
519B VAL 3.2 0.2 - - - -
520B ALA* 1.3 78.3 - - - +
522B VAL* 1.3 56.8 + - + +
524B VAL* 3.3 8.1 + - + +
525B GLU* 2.9 60.2 + - + +
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Residues in contact with VAL 522 (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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188B VAL* 5.9 5.2 - - + -
192B VAL* 4.3 27.8 - - + -
518B ASN* 3.1 20.0 + - + +
519B VAL* 3.1 11.6 + - + +
521B LYS* 1.3 76.4 - - + +
523B LEU* 1.3 63.3 + - + +
525B GLU* 3.2 14.5 + - - +
526B GLN* 2.9 56.4 + - - +
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Residues in contact with LEU 523 (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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145B LEU* 4.7 11.7 - - + -
192B VAL* 6.2 2.2 - - + -
195B THR* 5.5 7.9 - - + -
196B LEU* 6.2 0.4 - - + -
494B LEU* 6.2 2.7 - - + -
495B LEU* 6.0 1.6 - - + -
498B LEU* 4.5 13.0 - - + -
515B LEU* 3.8 38.4 - - + -
519B VAL* 3.0 22.1 + - + +
520B ALA* 3.2 7.2 + - - +
522B VAL* 1.3 82.2 - - + +
524B VAL* 1.3 57.9 + - - +
527B PHE* 2.9 56.9 + - + +
528B ASN 3.4 1.2 + - - -
529B ILE* 3.9 23.2 + - + +
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Residues in contact with VAL 524 (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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520B ALA* 3.0 23.7 + - + +
521B LYS* 3.6 7.6 - - - +
523B LEU* 1.3 75.2 - - - +
525B GLU* 1.3 64.0 + - + +
528B ASN* 2.8 44.7 + - - +
529B ILE* 3.5 24.7 - - + +
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Residues in contact with GLU 525 (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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521B LYS* 2.9 55.5 + - + +
522B VAL* 3.2 17.0 + - - +
524B VAL* 1.3 82.4 - - + +
526B GLN* 1.3 63.8 + - + +
528B ASN 4.9 0.3 + - - -
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Residues in contact with GLN 526 (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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192B VAL* 4.2 11.8 - - - +
196B LEU* 4.2 11.6 - - - +
503B LYS* 3.4 21.5 + - - +
522B VAL* 2.9 38.4 + - + +
525B GLU* 1.3 82.5 - - + +
527B PHE* 1.3 90.7 + - + +
528B ASN 3.9 0.2 - - - -
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Residues in contact with PHE 527 (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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192B VAL* 6.3 1.1 - - + -
196B LEU* 3.4 34.8 - - + -
498B LEU* 3.7 50.0 - - + +
502B VAL 4.5 1.5 - - - +
503B LYS* 3.4 32.3 - - + -
504B ASN 3.0 20.1 + - - -
505B ILE 4.6 0.5 + - - -
522B VAL* 6.0 0.2 - - + -
523B LEU* 2.9 40.7 + - + +
526B GLN* 1.3 110.9 - - + +
528B ASN* 1.3 68.6 + - - +
529B ILE* 3.2 5.9 + - + +
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Residues in contact with ASN 528 (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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503B LYS* 5.3 0.9 - - + -
504B ASN* 2.9 42.4 + - - +
506B HIS* 5.8 0.9 - - - -
523B LEU 3.4 0.2 + - - -
524B VAL* 2.8 31.7 + - - +
525B GLU 4.9 0.4 + - - -
526B GLN 3.9 0.2 - - - -
527B PHE* 1.3 79.1 - - - +
529B ILE* 1.3 67.5 + - - +
530B GLY* 3.6 1.0 + - - -
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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