Contacts of the strand formed by residues 483 - 492 (chain A) in PDB entry 1HMW
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 ASN 483 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A ARG* 3.7 1.2 - - - -
416A ASP* 2.8 38.2 + - + +
481A PRO 3.7 1.2 + - - -
482A GLU* 1.3 74.9 - - - +
484A ILE* 1.3 68.0 + - - +
485A THR* 3.8 11.7 - - - +
568A ASN* 3.5 26.5 + - - +
570A GLY* 2.7 42.6 + - - -
571A ALA* 3.9 7.8 - - + +
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Residues in contact with ILE 484 (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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413A THR* 3.8 27.4 - - + -
414A SER 3.7 4.3 - - - +
415A ARG* 3.4 37.0 - - + +
456A LEU* 4.1 12.8 - - + -
476A ILE* 4.2 6.5 - - + -
478A SER* 3.8 17.0 - - - +
482A GLU 3.9 5.8 - - - +
483A ASN* 1.3 81.7 + - - +
485A THR* 1.3 64.6 + - - +
569A HIS* 2.8 41.5 + - + +
570A GLY 3.0 7.5 + - - +
573A PRO* 3.5 28.3 - - + -
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Residues in contact with THR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASP 4.3 11.6 + - - -
408A LYS* 4.4 5.9 - - - +
412A ILE 3.8 0.5 - - - +
413A THR* 3.1 5.2 - - - +
414A SER 3.0 36.6 + - - -
416A ASP* 3.9 24.7 - - + +
483A ASN* 3.8 19.5 - - - +
484A ILE* 1.3 80.6 - - - +
486A THR* 1.3 64.0 + - - +
487A THR* 4.4 6.6 + - - -
566A TRP* 3.8 15.7 - - + -
567A ILE 3.1 9.4 - - - -
568A ASN* 3.8 13.0 - - - +
569A HIS* 4.0 1.6 - - - -
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Residues in contact with THR 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A GLY 4.3 4.5 - - - +
412A ILE 3.3 6.5 - - - +
413A THR* 2.7 19.9 + - - +
460A LYS* 4.0 4.5 - - - +
485A THR* 1.3 72.9 - - - +
487A THR* 1.3 63.9 + - - +
488A LEU* 3.7 4.5 + - + +
566A TRP* 3.3 1.8 - - - +
567A ILE* 2.8 35.8 + - + -
569A HIS* 2.7 28.9 + - - -
578A TYR* 3.4 35.7 - - + -
580A TYR* 4.4 13.0 - - + -
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Residues in contact with THR 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASP 4.6 0.2 + - - -
408A LYS* 3.2 49.3 - - + +
409A ILE 3.5 15.7 - - - +
410A PRO* 4.1 0.4 - - + -
411A GLY* 2.6 37.6 + - - -
412A ILE 2.9 11.3 + - - -
485A THR* 4.1 3.1 + - - -
486A THR* 1.3 72.5 - - - +
488A LEU* 1.3 58.2 + - - +
489A ASN* 3.5 28.3 - - - +
490A GLN* 4.5 1.1 - - + -
564A LYS* 5.1 2.5 - - + -
565A LEU 3.8 3.4 - - - +
566A TRP* 3.7 11.2 - - + +
580A TYR* 4.1 0.7 + - - -
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Residues in contact with LEU 488 (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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388A THR* 3.9 8.5 + - - -
390A ILE* 4.6 6.8 - - - +
411A GLY 3.8 6.8 + - - -
486A THR 3.8 7.2 - - - +
487A THR* 1.3 73.8 - - - +
489A ASN* 1.3 65.2 + - - +
527A TYR* 4.1 16.4 - - + -
529A PHE* 3.4 34.8 - - + -
565A LEU* 2.8 34.6 + - + +
566A TRP* 4.2 3.1 - - - -
567A ILE* 3.8 28.5 - - + -
580A TYR* 3.7 52.9 + - + -
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Residues in contact with ASN 489 (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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390A ILE* 4.0 17.0 + - - +
396A GLU* 6.3 0.2 - - - +
397A TYR* 3.0 33.9 + - - -
410A PRO* 3.6 7.3 - - - +
487A THR* 3.4 11.1 - - - +
488A LEU* 1.3 83.1 - - + +
490A GLN* 1.3 76.5 + - - +
491A SER* 3.9 15.5 + - - -
525A ILE* 4.5 6.9 - - - +
527A TYR* 3.0 31.1 + - + +
563A PHE* 4.0 9.6 - - + -
564A LYS* 3.4 2.3 - - - -
565A LEU* 3.1 26.2 + - - +
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Residues in contact with GLN 490 (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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397A TYR* 3.5 12.5 - - - -
400A ILE* 3.9 0.8 - - - +
404A TRP* 3.1 42.4 + - + +
405A GLU 2.8 39.2 + - - -
408A LYS* 2.9 29.9 + - - +
409A ILE 4.2 0.6 - - - +
410A PRO* 3.5 6.9 - - + +
489A ASN* 1.3 80.3 + - - +
491A SER* 1.3 58.3 + - - +
542A GLN* 3.3 15.6 + - - -
562A VAL* 3.7 14.8 - - + -
563A PHE 3.1 4.5 - - - -
564A LYS* 3.5 23.1 - - + +
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Residues in contact with SER 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU* 3.4 27.3 - - - +
397A TYR* 3.8 12.3 - - - -
400A ILE* 3.8 9.4 - - - -
489A ASN* 3.9 15.8 + - - -
490A GLN* 1.3 75.6 - - - +
492A TRP* 1.3 60.9 + - - +
522A HIS* 4.4 3.8 + - - -
523A ASP* 5.6 0.9 + - - -
562A VAL* 3.3 3.3 - - - +
563A PHE* 2.6 52.3 + - - +
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Residues in contact with TRP 492 (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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393A ARG* 5.1 5.4 + - - +
395A PRO 3.5 16.2 - - - -
396A GLU* 3.2 23.3 + - - +
397A TYR* 4.4 0.4 - - - -
398A TYR* 2.8 28.2 + - + +
399A ASN* 3.7 7.0 - - + -
400A ILE* 3.5 25.1 - - + +
403A VAL* 3.9 20.6 - - + -
491A SER* 1.3 76.9 + - - +
493A LEU* 1.3 68.1 + - - +
494A ASN* 3.2 8.7 + - + +
522A HIS* 3.5 11.6 - - - -
523A ASP* 4.9 2.9 - - - +
558A VAL* 6.1 0.9 - - + -
559A SER 4.8 3.6 - - - -
560A GLY* 3.8 23.1 - - - -
561A ASP 3.4 17.9 - - - -
562A VAL* 3.8 21.8 - - + -
563A PHE 4.1 0.2 - - - -
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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