Contacts of the strand formed by residues 66 - 74 (chain D) in PDB entry 3C5C
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 GLN 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A PHE 4.3 10.5 + - - -
161A PHE* 3.5 29.6 - - - -
62D THR* 3.2 3.7 - - - -
63D VAL 2.8 31.9 + - - +
64D ASP* 3.1 15.9 + - + +
65D HIS* 1.3 79.9 - - - +
67D PRO* 1.3 77.0 - - + +
68D VAL* 3.9 3.3 - - + +
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Residues in contact with PRO 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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171A HIS* 6.2 3.1 - - + -
174A HIS* 3.6 40.8 - - + +
19D LEU* 4.3 32.3 - - + +
61D GLU 3.3 7.6 - - - +
62D THR* 4.3 1.6 - - - +
66D GLN* 1.3 96.4 - - + +
68D VAL* 1.3 66.3 + - - +
69D HIS* 5.5 5.2 - - + +
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Residues in contact with VAL 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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19D LEU* 3.4 7.0 - - - +
21D VAL* 3.5 34.3 - - + -
60D GLU* 3.4 3.3 - - - +
61D GLU* 2.6 49.6 + - + +
63D VAL* 4.2 9.9 - - + +
66D GLN* 3.9 9.9 - - + +
67D PRO* 1.3 81.8 - - - +
69D HIS* 1.3 71.1 + - - +
70D LEU* 3.3 15.4 + - + +
180D VAL* 3.9 25.1 - - + -
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Residues in contact with HIS 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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170A GLU* 6.0 8.0 - - + +
19D LEU* 3.1 29.0 + - + +
20D GLU* 3.2 20.7 - - + +
21D VAL 3.0 21.8 + - - +
59D SER 3.6 5.6 - - - -
60D GLU* 3.9 31.7 + - + +
67D PRO* 5.6 5.6 - - + -
68D VAL* 1.3 75.1 + - - +
70D LEU* 1.3 60.9 + - - +
71D ARG* 3.8 10.9 + - - +
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Residues in contact with LEU 70 (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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21D VAL* 3.5 20.9 - - + +
23D LEU* 3.7 32.1 - - + -
40D PHE* 3.2 41.3 - - + -
57D TYR 3.6 0.7 - - - +
58D SER* 3.3 6.9 - - - -
59D SER* 2.7 45.6 + - - +
61D GLU* 3.9 11.4 - - + -
68D VAL* 3.3 5.4 + - + -
69D HIS* 1.3 72.1 - - - +
71D ARG* 1.3 63.8 + - - +
72D VAL* 3.9 15.5 - - + -
176D PHE* 4.9 2.2 - - + -
177D HIS* 6.0 0.4 - - - +
180D VAL* 4.0 19.7 - - + -
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Residues in contact with ARG 71 (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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20D GLU* 2.9 39.8 + - + +
21D VAL 2.9 12.1 + - - +
22D ASN* 3.9 2.5 - - - +
23D LEU* 2.7 34.0 + - - +
56D THR* 3.9 17.3 - - + -
57D TYR 3.3 2.9 - - - -
58D SER* 3.0 30.1 + - - -
69D HIS* 4.5 10.5 + - - +
70D LEU* 1.3 79.8 + - - +
72D VAL* 1.3 59.0 + - - +
73D MET 4.0 0.4 - - - -
90D TRP* 3.5 13.7 - - + -
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Residues in contact with VAL 72 (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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23D LEU* 3.3 5.6 - - + +
25D ILE* 3.5 38.4 - - + -
37D THR* 3.8 25.8 - - + +
40D PHE* 4.6 7.9 - - + -
41D LEU* 5.1 4.5 - - + -
56D THR* 3.2 3.6 - - - -
57D TYR* 2.8 45.1 + - + +
59D SER* 5.5 0.7 - - - +
70D LEU* 3.9 28.0 - - + -
71D ARG* 1.3 73.9 - - - +
73D MET* 1.3 59.5 + - - +
74D ASP 3.5 3.3 + - - -
176D PHE* 4.2 15.7 - - + -
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Residues in contact with MET 73 (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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23D LEU 2.8 10.2 + - - +
24D ALA* 4.3 1.8 - - - -
25D ILE* 2.8 30.7 + - - +
54D GLU* 4.3 15.0 - - + +
55D ASP 3.6 6.5 - - - +
56D THR* 3.6 20.2 - - - +
72D VAL* 1.3 70.5 - - - +
74D ASP* 1.3 58.3 + - - +
75D THR* 3.3 21.6 + - + +
86D ARG* 3.7 24.9 - - + +
87D TYR* 4.0 24.0 - - - -
90D TRP* 3.5 38.6 - - + +
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Residues in contact with ASP 74 (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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25D ILE* 4.4 6.2 - - - +
33D LYS* 3.4 24.6 - - - +
34D SER* 2.5 40.5 + - - -
37D THR* 4.0 14.8 + - + +
38D VAL* 5.8 0.3 - - - +
49D TYR* 4.3 0.7 - - - -
53D LEU 4.1 5.6 - - - +
54D GLU* 3.3 23.4 - - - +
55D ASP 3.0 13.8 + - - +
57D TYR* 3.8 25.3 + - + -
72D VAL 3.5 2.2 + - - -
73D MET* 1.3 70.0 - - - +
75D THR* 1.3 64.1 + - - +
202D MG 4.1 0.6 - - - -
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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