Contacts of the strand formed by residues 24 - 35 (chain D) in PDB entry 2HYE
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 VAL 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520C PRO 4.2 2.8 - - - +
521C ILE* 3.9 25.1 - - + +
547C MET* 5.8 11.4 - - + -
576C ALA* 4.2 11.7 - - + -
577C VAL 3.4 5.8 - - - +
578C LEU* 4.8 1.8 - - + -
579C LYS* 5.6 0.4 - - - -
596C THR* 4.5 13.9 - - + -
600C LEU* 4.4 17.9 - - + -
23D GLU* 1.3 88.2 - - - +
25D LYS* 1.3 70.2 + - - +
26D LYS 3.3 24.2 - - - +
27D TRP* 4.3 11.7 - - + -
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Residues in contact with LYS 25 (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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520C PRO* 4.0 18.0 + - - +
521C ILE* 4.1 0.3 - - - -
522C ASP* 3.2 26.3 + - - +
577C VAL* 2.6 30.4 + - + +
578C LEU* 4.7 0.6 - - - +
579C LYS* 3.3 49.7 - - + +
588C GLU* 5.2 6.1 - - - +
23D GLU* 4.2 2.6 + - - +
24D VAL* 1.3 80.2 + - - +
26D LYS* 1.3 67.4 + - + +
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Residues in contact with LYS 26 (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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521C ILE* 4.7 0.2 - - - -
522C ASP* 3.4 28.4 + - + +
524C THR* 6.1 1.3 - - - +
576C ALA* 3.2 5.7 - - - +
577C VAL* 3.0 46.5 + - + +
666C ARG* 6.3 0.9 - - - +
24D VAL* 3.3 7.7 - - - +
25D LYS* 1.3 89.7 - - + +
27D TRP* 1.3 62.3 + - - +
28D ASN* 4.7 13.2 - - - +
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Residues in contact with TRP 27 (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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521C ILE* 3.7 16.2 - - + -
522C ASP 3.0 8.1 + - - +
523C LEU* 3.2 47.4 - - + +
524C THR 3.2 7.3 + - - -
543C LEU* 5.1 4.0 - - + -
547C MET* 3.5 45.0 - - + +
550C LEU* 3.7 35.2 - - + -
551C GLN* 3.3 32.3 - - + -
575C HIS 4.1 2.7 - - - -
576C ALA* 3.8 17.3 - - + -
593C LEU* 3.2 33.1 - - + +
596C THR* 6.5 0.4 - - + -
24D VAL* 4.3 6.1 - - + -
26D LYS* 1.3 78.0 - - - +
28D ASN* 1.3 66.4 + - - +
29D ALA* 4.5 11.9 - - + -
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Residues in contact with ASN 28 (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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524C THR* 3.2 30.5 + - - +
574C GLY* 3.6 4.4 - - - -
575C HIS* 2.9 71.0 + - + +
576C ALA* 4.5 0.6 - - - +
593C LEU* 4.9 0.2 - - - +
26D LYS* 4.3 12.5 - - - +
27D TRP* 1.3 85.2 + - - +
29D ALA* 1.3 61.6 + - - +
30D VAL* 5.3 1.1 - - + -
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Residues in contact with ALA 29 (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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523C LEU* 4.1 19.7 - - + -
524C THR 3.0 7.1 + - - +
525C VAL* 3.5 6.7 - - + -
526C ASN* 3.0 25.5 + - - +
551C GLN* 5.0 0.7 - - + +
569C TRP* 4.1 20.2 - - + +
574C GLY* 4.9 2.7 - - - -
593C LEU* 5.6 2.9 - - + -
27D TRP* 3.7 18.3 + - + +
28D ASN* 1.3 74.6 - - - +
30D VAL* 1.3 69.5 + - - +
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Residues in contact with VAL 30 (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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462C LEU* 4.2 20.0 - - + +
525C VAL* 5.1 0.2 - - - -
526C ASN* 3.4 8.7 - - + +
528C LEU* 3.5 30.7 - - + -
569C TRP* 3.1 10.5 - - - -
570C GLN* 2.9 36.8 + - + +
573C LEU* 3.9 43.1 - - + +
574C GLY* 4.5 1.5 - - - +
575C HIS* 5.9 2.7 - - + +
593C LEU* 6.2 0.2 - - - +
28D ASN* 5.2 1.3 - - + +
29D ALA* 1.3 85.0 - - - +
31D ALA* 1.3 65.9 + - - +
32D LEU* 5.3 0.4 - - + -
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Residues in contact with ALA 31 (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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525C VAL* 5.2 1.8 - - + -
526C ASN 3.1 6.5 + - - +
527C ILE* 3.4 22.2 - - + +
528C LEU* 2.8 32.4 + - - +
567C LEU* 4.5 3.4 - - + -
568C GLN 3.7 17.5 - - - +
569C TRP* 3.7 28.0 - - + +
570C GLN 4.3 0.7 - - - +
30D VAL* 1.3 78.8 - - - +
32D LEU* 1.3 59.6 + - - +
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Residues in contact with LEU 32 (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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528C LEU* 3.1 38.4 - - + +
530C MET* 3.3 36.5 - - + +
533C TRP* 4.9 7.6 - - + -
534C PRO 5.4 1.1 - - - +
536C TYR* 4.6 24.0 - - + +
566C LYS 3.6 1.0 - - - +
567C LEU* 3.6 5.0 - - - -
568C GLN* 3.0 54.9 + - - +
570C GLN* 3.7 25.1 - - + -
573C LEU* 5.3 0.7 - - + -
30D VAL* 5.3 1.3 - - + -
31D ALA* 1.3 75.4 - - - +
33D TRP* 1.3 60.4 + - - +
34D ALA 4.3 0.2 + - - -
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Residues in contact with TRP 33 (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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497C ASP* 4.3 3.7 + - - -
527C ILE* 4.4 9.2 - - + +
528C LEU 2.9 32.2 + - - -
529C THR* 2.8 35.2 + - + +
530C MET* 3.2 24.9 + - - +
558C TYR* 4.1 17.3 - - + +
565C ARG* 3.4 47.3 - - - +
566C LYS 3.1 11.2 - - - +
567C LEU* 3.9 15.0 - - + -
31D ALA 4.2 0.6 + - - -
32D LEU* 1.3 73.9 - - - +
34D ALA* 1.3 77.8 + - - +
35D TRP* 3.6 34.3 - + - -
75D CYS 4.9 0.2 - - - -
76D ASN* 3.2 31.6 + - + -
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Residues in contact with ALA 34 (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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530C MET* 4.5 10.3 - - - -
565C ARG* 3.6 0.3 - - - -
566C LYS* 2.8 48.4 + - - +
32D LEU 5.5 0.2 - - - +
33D TRP* 1.3 86.2 - - - +
35D TRP* 1.3 66.4 + - - +
72D TRP* 4.5 21.8 - - + -
76D ASN* 3.9 5.6 - - - +
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Residues in contact with TRP 35 (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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563C SER 4.9 5.8 - - - -
564C GLY* 3.1 32.8 - - - +
565C ARG* 3.9 25.1 - - + +
566C LYS* 4.0 10.3 + - - -
33D TRP* 3.6 19.0 - + - -
34D ALA* 1.3 77.0 - - - +
36D ASP* 1.3 61.2 + - - +
37D ILE* 3.3 15.6 + - + +
75D CYS 3.0 26.2 + - - -
76D ASN* 3.4 24.1 + - - +
77D HIS* 3.1 54.1 + + + +
97D ASP* 4.7 4.3 - - - -
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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