Contacts of the helix formed by residues 516 - 528 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ASP* 3.8 15.7 - - - -
138A ASP* 2.8 26.7 + - - -
140A ARG* 6.2 0.2 - - - -
141A SER* 3.1 20.2 + - - -
514A PHE 3.7 0.4 + - - -
515A LEU* 1.3 74.7 - - - +
517A PRO* 1.3 76.9 - - - +
519A VAL* 3.1 18.8 + - - +
520A ALA* 2.8 21.2 + - - +
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Residues in contact with PRO 517 (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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137A ASP* 5.8 4.0 - - + +
515A LEU 3.9 1.8 - - - +
516A SER* 1.3 87.2 - - - +
518A ASN* 1.3 62.6 + - - +
520A ALA* 3.4 6.9 + - + +
521A LYS* 2.9 28.1 + - - +
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Residues in contact with ASN 518 (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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138A ASP* 3.0 34.0 + - - +
516A SER* 3.2 1.8 + - - -
517A PRO* 1.3 80.4 - - - +
519A VAL* 1.3 64.8 + - - +
521A LYS* 3.4 15.4 + - - +
522A VAL* 3.2 26.0 + - - +
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Residues in contact with VAL 519 (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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138A ASP* 4.1 9.9 - - + +
141A SER* 3.5 23.3 - - - +
142A LEU* 3.8 39.7 - - + -
145A LEU* 4.6 4.5 - - + -
188A VAL* 6.0 0.9 - - + -
192A VAL* 6.0 0.9 - - + -
515A LEU* 4.0 19.5 - - + -
516A SER* 3.1 21.0 + - - +
518A ASN* 1.3 74.6 - - - +
520A ALA* 1.3 67.3 + - - +
522A VAL* 3.2 10.2 + - + +
523A LEU* 3.1 28.2 + - + +
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Residues in contact with ALA 520 (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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511A LEU* 6.1 4.7 - - + -
515A LEU* 4.4 21.2 - - + +
516A SER 2.8 16.1 + - - +
517A PRO* 3.6 9.0 - - + +
519A VAL* 1.3 77.9 - - - +
521A LYS* 1.3 55.5 + - - +
523A LEU* 3.2 10.2 + - - +
524A VAL* 2.9 36.9 + - + +
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Residues in contact with LYS 521 (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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517A PRO 2.9 17.8 + - - +
518A ASN* 3.6 17.2 - - - +
519A VAL 3.2 0.2 - - - -
520A ALA* 1.3 76.5 - - - +
522A VAL* 1.3 57.1 + - + +
524A VAL* 3.3 6.0 + - + +
525A GLU* 2.8 66.3 + - + +
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Residues in contact with VAL 522 (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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192A VAL* 4.7 27.8 - - + -
518A ASN 3.2 13.4 + - - +
519A VAL* 3.2 12.2 + - + +
521A LYS* 1.3 77.1 - - + +
523A LEU* 1.3 65.6 + - + +
525A GLU* 4.3 10.3 - - - +
526A GLN* 2.9 44.8 + - + +
527A PHE* 5.3 4.5 - - + -
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Residues in contact with LEU 523 (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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145A LEU* 5.2 8.1 - - + -
195A THR* 6.1 3.8 - - + -
494A LEU* 5.9 3.6 - - + -
495A LEU* 6.3 0.7 - - + -
498A LEU* 4.1 17.7 - - + -
515A LEU* 4.0 37.7 - - + -
519A VAL* 3.1 19.9 + - + +
520A ALA* 3.2 7.8 + - - +
522A VAL* 1.3 81.3 - - + +
524A VAL* 1.3 58.1 + - + +
527A PHE* 3.0 48.6 + - + +
528A ASN 3.1 6.2 + - - -
529A ILE* 3.3 27.6 + - + -
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Residues in contact with VAL 524 (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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511A LEU* 6.5 1.1 - - + -
520A ALA* 2.9 23.3 + - + +
521A LYS* 3.7 8.1 - - + +
523A LEU* 1.3 78.1 - - + +
525A GLU* 1.3 64.4 + - + +
528A ASN* 2.9 34.5 + - - +
529A ILE* 3.5 26.2 - - + +
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Residues in contact with GLU 525 (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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503A LYS* 5.3 3.6 + - - -
521A LYS* 2.8 60.7 + - + +
522A VAL* 4.0 8.4 - - - +
524A VAL* 1.3 81.2 - - + +
526A GLN* 1.3 77.4 + - - +
528A ASN* 4.8 0.3 + - - +
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Residues in contact with GLN 526 (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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503A LYS* 3.5 21.0 + - - +
522A VAL* 2.9 28.6 + - + +
525A GLU* 1.3 95.4 + - + +
527A PHE* 1.3 82.6 + - + +
528A ASN 3.7 0.4 - - - -
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Residues in contact with PHE 527 (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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192A VAL* 6.5 0.7 - - + -
196A LEU* 3.7 34.1 - - + -
498A LEU* 3.6 49.1 - - + +
501A GLY* 5.4 4.5 - - - -
502A VAL 4.3 8.5 - - - +
503A LYS* 3.3 15.6 - - + -
504A ASN 2.9 20.4 + - - -
505A ILE 4.4 0.2 + - - -
522A VAL* 4.9 4.9 - - + -
523A LEU* 3.0 38.1 + - + +
526A GLN* 1.3 97.8 - - + +
528A ASN* 1.3 69.0 + - - +
529A ILE* 3.2 7.6 + - + +
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Residues in contact with ASN 528 (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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503A LYS* 4.8 7.6 - - - +
504A ASN* 2.8 43.3 - - - +
506A HIS* 5.7 3.5 + - - -
523A LEU 3.1 0.4 + - - -
524A VAL* 2.9 28.8 + - - +
525A GLU 4.6 0.2 - - - -
526A GLN 3.7 1.0 - - - -
527A PHE* 1.3 78.1 - - - +
529A ILE* 1.3 68.7 + - - +
530A GLY* 3.5 1.9 + - - -
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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