Contacts of the strand formed by residues 41 - 48 (chain D) in PDB entry 2HQH
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 ARG 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D ARG* 3.7 12.2 - - - +
33D VAL 3.3 7.0 - - - +
34D GLU* 4.5 8.1 + - + -
39D GLY 3.4 13.1 + - - +
40D HIS* 1.3 74.8 - - - +
42D GLY* 1.3 59.0 + - - +
62D LEU* 3.6 6.7 - - - +
63D ASP* 2.8 41.4 + - + +
64D GLU 4.5 0.3 + - - -
97D PHE* 3.4 43.6 - - + -
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Residues in contact with GLY 42 (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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32D ARG* 3.4 19.5 + - - +
33D VAL* 2.8 32.2 + - - +
40D HIS 4.2 0.2 + - - -
41D ARG* 1.3 77.2 - - - +
43D THR* 1.3 63.6 + - - -
60D VAL* 4.0 10.1 - - - -
61D ILE 3.2 13.9 - - - -
62D LEU* 3.9 3.3 - - - +
63D ASP* 3.8 1.6 - - - -
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Residues in contact with THR 43 (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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30D GLY* 3.7 21.3 - - - +
31D SER 3.3 11.0 - - - +
32D ARG* 3.3 25.4 + - - +
42D GLY* 1.3 71.5 - - - -
44D VAL* 1.3 75.4 + - - +
45D ALA* 3.3 1.1 + - + +
60D VAL* 3.8 4.0 - - - +
61D ILE* 2.8 42.0 + - + +
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Residues in contact with VAL 44 (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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26D PRO* 3.9 9.6 - - + +
28D ARG 3.3 19.5 - - - +
29D VAL* 3.4 4.1 - - - +
30D GLY 2.8 26.9 + - - -
31D SER* 2.9 18.8 + - - +
33D VAL* 3.7 26.7 - - + -
42D GLY 4.3 0.2 - - - -
43D THR* 1.3 74.0 - - - +
45D ALA* 1.3 60.4 + - - +
46D TYR 3.7 9.2 - - - +
47D VAL* 3.4 32.8 - - + -
58D VAL* 3.9 17.5 - - + -
59D GLY 3.6 5.8 - - - +
60D VAL* 4.4 1.6 - - + +
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Residues in contact with ALA 45 (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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29D VAL* 4.0 19.9 - - - +
43D THR 3.3 0.6 + - - -
44D VAL* 1.3 75.5 - - - +
46D TYR* 1.3 65.0 + - - +
59D GLY 2.7 8.0 + - - +
61D ILE* 3.7 36.1 - - + -
78D TYR 5.0 0.5 - - - +
79D PHE* 3.8 27.0 - - + +
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Residues in contact with TYR 46 (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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29D VAL* 4.1 4.9 - - - +
44D VAL* 3.6 2.5 - - - +
45D ALA* 1.3 82.5 - - - +
47D VAL* 1.3 72.2 + - - +
48D GLY* 3.7 23.7 - - - -
49D ALA 2.5 31.3 + - - -
50D THR* 4.0 7.9 - - + -
57D TRP 4.2 2.5 - - - -
58D VAL* 3.3 2.6 - - - -
59D GLY* 2.6 32.8 + - - +
78D TYR* 3.6 41.3 - + + -
79D PHE* 4.0 17.0 - - + -
88D PHE* 3.8 14.4 - + - -
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Residues in contact with VAL 47 (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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26D PRO 3.7 16.2 - - - +
27D LEU 4.7 4.9 - - - +
28D ARG* 4.4 2.5 - - - -
29D VAL* 4.3 19.1 - - + +
44D VAL* 3.4 21.8 - - + -
46D TYR* 1.3 89.4 - - - +
48D GLY* 1.3 58.3 + - - +
56D LYS* 3.5 33.7 - - + +
57D TRP 3.4 4.7 - - - +
58D VAL* 4.5 5.6 - - + -
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Residues in contact with GLY 48 (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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46D TYR* 3.7 7.5 - - - -
47D VAL* 1.3 78.3 - - - +
49D ALA* 1.3 65.2 + - - -
56D LYS* 4.4 10.0 - - - +
57D TRP* 2.9 38.7 + - - +
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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