Contacts of the strand formed by residues 61 - 69 (chain D) in PDB entry 2HHL
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 THR 61 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D GLU* 4.1 0.7 - - - -
58D ILE 2.8 38.6 + - - -
59D ASP* 3.2 4.9 + - - -
60D GLY* 1.3 77.6 - - - +
62D ILE* 1.3 66.2 + - - +
63D HIS* 3.2 25.6 - - + +
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Residues in contact with ILE 62 (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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55D PRO* 3.7 31.2 - - + -
56D VAL 3.5 5.8 - - - +
57D GLU* 3.1 42.8 - - + +
60D GLY 4.1 2.2 + - - +
61D THR* 1.3 80.1 - - - +
63D HIS* 1.3 68.3 + - - +
64D GLN* 6.1 1.1 - - + -
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Residues in contact with HIS 63 (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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44D PHE* 3.7 40.6 - + + -
55D PRO* 3.6 0.3 - - - +
56D VAL* 2.8 39.1 + - + +
58D ILE* 4.0 23.0 + - + +
61D THR* 3.2 36.9 + - + +
62D ILE* 1.3 79.5 - - - +
64D GLN* 1.3 61.8 + - - +
65D VAL* 3.6 0.7 + - + +
901D KEG 5.6 0.7 - - - -
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Residues in contact with GLN 64 (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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44D PHE* 3.3 29.6 - - - +
53D ILE* 3.5 26.4 - - + +
54D VAL 3.8 4.3 - - - -
55D PRO* 4.6 6.7 - - + +
62D ILE* 6.1 1.1 - - + -
63D HIS* 1.3 71.2 - - - +
65D VAL* 1.3 61.2 + - - +
66D TYR* 2.8 37.1 + - + -
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Residues in contact with VAL 65 (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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42D SER* 3.6 28.7 - - - +
43D SER* 3.6 9.4 - - - +
44D PHE* 3.7 24.9 - - + -
52D PHE 3.8 0.5 - - - +
53D ILE* 3.4 6.0 - - - -
54D VAL* 2.8 40.3 + - + +
56D VAL* 3.5 31.6 - - + -
64D GLN* 1.3 72.6 - - - +
66D TYR* 1.3 62.8 + - - +
67D VAL* 3.8 4.9 + - + +
96D TYR* 3.8 19.7 - - + -
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Residues in contact with TYR 66 (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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42D SER* 3.0 5.2 - - - -
43D SER 2.7 39.9 + - - +
44D PHE 3.6 17.9 - - - -
45D LYS 3.6 13.0 - - - +
46D PRO* 3.5 40.2 - - + +
47D ILE* 3.4 29.2 - - + +
50D ALA* 3.9 8.5 - - + -
52D PHE 3.7 2.0 - - - -
53D ILE* 3.8 32.3 - - + -
64D GLN* 2.8 39.4 + - + -
65D VAL* 1.3 72.7 - - - +
67D VAL* 1.3 59.5 + - - +
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Residues in contact with VAL 67 (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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40D VAL* 3.7 27.4 - - + -
42D SER* 3.4 26.2 - - - +
47D ILE* 4.4 2.0 - - - -
50D ALA* 3.6 1.4 - - - +
51D ASP* 2.8 32.4 + - - +
52D PHE* 2.9 46.6 + - + +
54D VAL* 4.3 8.7 - - + -
65D VAL* 4.0 13.5 - - + +
66D TYR* 1.3 74.3 - - - +
68D LEU* 1.3 58.1 + - - +
100D VAL* 3.9 24.2 - - + -
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Residues in contact with LEU 68 (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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40D VAL* 3.2 6.5 - - - +
41D HIS 2.8 41.4 + - - +
47D ILE* 3.9 27.1 - - + +
49D ASN* 3.4 44.4 - - - +
50D ALA* 4.3 0.9 - - - -
51D ASP* 3.6 10.3 - - - +
67D VAL* 1.3 75.3 - - - +
69D LYS* 1.3 63.5 + - - +
163D TRP* 3.5 18.0 - - + -
164D PHE 3.8 18.8 - - - +
165D ASP* 4.2 14.8 - - + +
167D MET* 4.9 9.9 - - - -
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Residues in contact with LYS 69 (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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39D LEU 4.0 4.0 - - - +
40D VAL* 4.2 2.5 - - + -
51D ASP* 2.8 40.3 + - + +
52D PHE* 3.6 32.2 - - + -
68D LEU* 1.3 72.4 - - - +
70D ARG* 1.3 65.1 + - - +
71D PRO* 3.5 2.4 - - - +
73D VAL* 3.4 27.6 - - + +
74D ASP* 3.3 30.3 + - - -
104D LEU* 4.2 11.0 - - + -
106D ARG* 4.2 7.0 - - - +
163D TRP* 3.4 10.4 - - - -
167D MET* 4.0 7.8 - - - +
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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