Contacts of the strand formed by residues 513 - 520 (chain A) in PDB entry 2HD5
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 ALA 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A LEU* 3.5 8.0 - - + +
408A ARG* 2.8 30.4 + - - +
427A PHE* 3.5 33.2 - - + -
453A VAL* 3.7 17.3 - - + -
455A ASN* 3.5 12.9 + - - +
493A VAL 5.5 0.4 - - - +
495A THR* 3.4 8.9 + - - +
496A SER 3.3 1.8 - - - -
512A ASP* 1.3 74.7 - - - +
514A TYR* 1.3 59.4 + - - +
516A LEU* 4.0 6.3 - - + -
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Residues in contact with TYR 514 (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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295A ASP* 2.6 35.3 + - - -
297A GLN 4.5 5.2 - - - -
405A HIS* 2.8 29.8 + + - -
406A LEU* 3.0 57.9 + - - +
408A ARG* 4.4 6.5 - - - +
409A PHE* 3.5 16.6 - + - -
454A SER 3.0 11.3 + - - +
456A HIS* 4.3 9.0 - - + +
465A TYR* 3.5 29.8 - + - -
512A ASP 3.3 6.3 + - - +
513A ALA* 1.3 75.8 - - - +
515A LEU* 1.3 70.7 + - + +
516A LEU 4.3 0.2 - - - -
42B ARG* 4.0 0.5 + - - -
73B LEU* 3.6 30.7 - - + -
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Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 3.7 29.2 - - + -
296A ALA* 4.1 5.8 - - + -
297A GLN* 3.8 31.4 - - + +
300A LEU* 4.5 6.5 - - + -
403A VAL* 3.9 18.6 - - + -
404A LEU 3.4 0.7 - - - -
405A HIS* 3.5 40.8 - - + -
453A VAL* 3.2 8.3 - - - +
454A SER* 2.8 39.4 + - - -
514A TYR* 1.3 84.7 - - + +
516A LEU* 1.3 63.0 + - - +
517A PHE* 4.0 9.2 - - + -
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Residues in contact with LEU 516 (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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360A LEU* 3.9 27.1 - - + -
402A LEU 3.5 1.6 - - - +
403A VAL* 3.3 5.5 - - - +
404A LEU* 2.8 44.6 + - + +
406A LEU* 4.7 14.1 - - + -
425A VAL* 5.7 0.2 - - + -
427A PHE* 3.8 44.0 - - + -
450A LEU* 4.2 1.6 - - + -
452A ALA 3.8 2.7 - - - -
453A VAL* 4.1 7.6 - - + -
513A ALA* 4.0 25.8 - - + -
515A LEU* 1.3 82.1 - - - +
517A PHE* 1.3 61.3 + - - +
518A TYR* 3.8 15.7 - - + -
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Residues in contact with PHE 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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228A ILE* 4.2 16.8 - - + -
231A CYS* 3.6 38.6 - - + -
232A LEU* 4.4 16.4 - - + -
235A THR* 4.8 1.1 - - - -
300A LEU* 4.3 15.5 - - + -
324A PHE* 5.0 1.3 - + - -
401A ILE* 4.7 2.0 - - + -
402A LEU 3.8 2.9 - - - -
403A VAL* 3.8 26.5 - - + -
450A LEU* 3.4 3.7 - - - +
451A TYR* 2.9 55.4 + + + -
452A ALA* 2.9 29.7 + - + +
454A SER* 4.5 2.7 - - - -
515A LEU* 4.0 23.3 - - + -
516A LEU* 1.3 74.1 - - - +
518A TYR* 1.3 61.3 + - - +
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Residues in contact with TYR 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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360A LEU* 3.6 8.7 - - + +
401A ILE* 3.4 7.4 - - - +
402A LEU* 2.8 40.5 + - + +
404A LEU* 3.9 11.4 - - + -
427A PHE* 3.4 23.0 - - - +
428A PRO* 2.7 34.9 + - - +
429A LEU 4.9 0.4 - - - -
431A LEU* 3.8 34.1 - - + -
448A TYR* 3.7 25.6 - - + -
449A ASN* 3.4 7.2 - - - -
450A LEU* 3.3 38.1 - - + -
451A TYR* 3.8 2.7 - - - -
516A LEU* 3.8 17.0 - - + -
517A PHE* 1.3 74.7 - - - +
519A GLU* 1.3 59.9 + - - +
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Residues in contact with GLU 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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236A ARG* 4.6 27.1 + - - +
237A GLU* 5.6 1.4 - - - +
400A LYS 3.6 4.0 - - - -
401A ILE* 4.0 13.4 - - + +
448A TYR* 3.3 5.0 - - - -
449A ASN* 2.8 52.3 + - + +
450A LEU 4.9 1.0 - - - +
451A TYR* 3.8 31.8 - - + +
470A ARG* 5.2 8.7 + - - -
518A TYR* 1.3 73.4 - - - +
520A LEU* 1.3 69.0 + - - +
521A ALA* 4.4 0.2 - - - -
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Residues in contact with LEU 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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398A PHE* 4.9 9.0 - - + +
399A PRO 4.0 12.3 - - - +
400A LYS* 2.9 30.4 + - + +
443A HIS 5.0 2.9 - - - +
446A ALA* 4.2 8.7 - - + -
447A VAL 3.6 20.6 - - - +
448A TYR* 3.4 32.4 - - + +
519A GLU* 1.3 76.3 - - - +
521A ALA* 1.3 70.6 + - - +
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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