Contacts of the strand formed by residues 24 - 29 (chain D) in PDB entry 2H5X
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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2A ILE* 4.1 24.7 - - + -
4A SER 3.6 6.3 - - - +
5A VAL* 5.3 3.4 - - + -
21A ALA* 4.0 7.6 - - + -
26A TYR* 3.5 29.4 - - + +
20D GLU* 3.3 1.4 - - - +
21D ALA 2.8 34.7 + - - +
22D ALA* 3.0 15.7 - - + +
23D GLY* 1.3 80.0 - - - +
25D GLY* 1.3 60.8 + - - +
26D TYR* 3.4 42.6 - - + +
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Residues in contact with GLY 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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2A ILE* 3.7 3.3 - - - -
3A ALA* 2.7 32.6 + - - -
4A SER* 2.8 33.4 + - - -
18D VAL* 4.2 7.6 - - - -
19D ILE 3.4 8.7 - - - -
20D GLU* 3.9 8.9 - - - +
23D GLY 3.9 1.2 + - - -
24D VAL* 1.3 72.9 - - - +
26D TYR* 1.3 56.5 + - - -
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Residues in contact with TYR 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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1A MET* 3.3 40.6 - - + +
2A ILE* 4.6 6.2 - - + +
3A ALA* 4.5 0.7 - - - -
26A TYR* 5.2 1.9 + - - -
24C VAL* 3.8 28.8 - - + +
26C TYR* 5.3 2.1 + - - -
2D ILE* 4.1 9.7 - - + +
5D VAL* 4.1 20.9 - - + -
18D VAL* 3.3 5.1 - - - -
19D ILE 2.9 34.6 + - - +
21D ALA* 4.1 7.8 + - + -
24D VAL* 3.4 46.9 - - + +
25D GLY* 1.3 72.0 - - - -
27D ARG* 1.3 62.0 + - - +
28D VAL* 3.3 5.2 + - + +
59D LEU* 4.1 20.9 - - + -
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Residues in contact with ARG 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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1A MET* 2.9 28.1 + - - +
3A ALA* 4.1 17.2 - - + +
68A ARG* 5.6 5.7 - - - +
15D ASP* 3.8 12.1 + - - -
16D HIS* 3.2 56.5 + - + +
17D VAL 3.4 4.3 - - - -
18D VAL* 4.6 2.0 - - + +
25D GLY 4.0 1.2 + - - -
26D TYR* 1.3 70.7 - - - +
28D VAL* 1.3 60.7 + - - +
29D ASN* 3.2 28.0 + - - +
58D THR* 5.7 0.8 - - - +
59D LEU* 3.7 21.1 + - - +
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Residues in contact with VAL 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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5D VAL* 4.6 6.3 - - + -
16D HIS* 3.3 2.2 - - - -
17D VAL* 2.7 46.0 + - + +
19D ILE* 4.6 17.0 - - + -
26D TYR* 4.0 12.8 - - + +
27D ARG* 1.3 76.8 - - - +
29D ASN* 1.3 61.0 + - - +
30D ALA* 3.7 0.5 + - - +
46D LEU* 3.8 15.9 - - + -
48D THR* 3.8 14.6 - - + -
59D LEU* 3.9 18.2 - - + +
60D TYR 3.9 1.3 - - - +
61D GLY* 3.1 38.1 - - - +
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Residues in contact with ASN 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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15D ASP* 3.8 6.5 - - - +
16D HIS* 3.6 8.4 - - - +
27D ARG* 3.2 38.1 + - - +
28D VAL* 1.3 72.6 - - - +
30D ALA* 1.3 58.4 + - - +
58D THR* 2.9 35.4 - - - +
59D LEU 3.0 16.8 + - - +
60D TYR* 3.4 20.3 - - + -
61D GLY 2.7 27.5 + - - -
86D MET* 4.1 6.4 - - + +
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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