Contacts of the strand formed by residues 519 - 523 (chain D) in PDB entry 1M7X
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 PHE 519 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D TYR* 4.4 0.3 - - - -
480D LYS* 3.1 32.1 - - + -
481D TRP 3.9 0.9 - - - -
482D ASN* 3.3 44.6 - - + +
513D TYR* 3.5 50.0 - + - -
514D ASN* 4.0 15.7 - - - +
516D THR* 4.5 0.4 - - - -
517D GLU* 3.3 44.6 + - + -
518D ASN* 1.3 74.1 - - - +
520D VAL* 1.3 63.9 + - - +
521D LEU* 4.1 5.4 - - + -
561D PRO 5.4 0.4 - - - +
562D GLY* 3.4 7.4 - - - -
563D LYS* 3.0 25.6 + - - +
621D PHE* 3.6 7.5 - - - -
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Residues in contact with VAL 520 (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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243D ILE* 6.3 0.2 - - + -
245D ILE* 4.2 13.9 - - + -
456D MET* 4.2 12.1 - - - -
479D TYR* 3.9 31.4 - - + -
480D LYS 3.0 8.4 + - - +
481D TRP* 3.7 20.6 - - + +
482D ASN* 2.9 13.9 + - - +
519D PHE* 1.3 78.4 - - - +
521D LEU* 1.3 61.8 + - - +
522D PRO* 2.9 16.6 - - - +
563D LYS* 3.5 17.3 - - + +
565D LEU* 3.8 29.4 - - + +
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Residues in contact with LEU 521 (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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482D ASN* 4.1 15.7 - - + +
485D TRP* 3.7 48.5 - - + -
519D PHE* 4.8 1.3 - - + -
520D VAL* 1.3 71.9 - - - +
522D PRO* 1.4 61.9 - - - +
557D MET* 3.1 48.0 - - + +
560D PHE* 3.7 27.8 - - + +
561D PRO 3.6 17.5 - - - +
562D GLY* 4.4 3.8 - - - -
563D LYS 2.6 17.0 + - - +
564D LYS* 3.8 3.1 - - - +
565D LEU 3.1 13.5 + - - -
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Residues in contact with PRO 522 (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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481D TRP* 4.0 35.9 - - + -
482D ASN 3.3 30.1 - - - +
483D LEU* 4.8 4.9 - - + -
485D TRP* 4.5 3.7 - - + -
486D MET* 3.2 27.3 - - + +
520D VAL 2.9 17.7 - - - +
521D LEU* 1.4 79.3 - - - +
523D LEU* 1.3 65.2 + - - +
524D SER* 3.6 4.9 + - - +
565D LEU* 3.7 18.6 - - + +
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Residues in contact with LEU 523 (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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485D TRP* 4.2 6.5 - - + -
486D MET* 4.2 13.5 - - + -
490D LEU* 4.2 8.3 - - + -
521D LEU 4.1 0.2 + - - -
522D PRO* 1.3 82.8 - - - +
524D SER* 1.3 55.5 + - - +
527D GLU* 5.3 2.5 - - + -
535D ILE* 4.2 19.5 - - + -
553D TYR* 3.6 29.8 - - + +
554D TYR* 3.8 17.5 - - + +
557D MET* 3.5 24.9 - - + +
565D LEU* 3.0 9.4 + - - +
566D LEU* 3.6 25.7 - - + -
567D PHE 2.8 31.7 + - - -
570D ASN* 3.2 9.6 - - - +
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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