Contacts of the strand formed by residues 22 - 30 (chain H) in PDB entry 3B4V
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 CYS 22 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13H TRP* 3.7 21.2 - - + -
14H LEU 3.7 4.5 - - - -
15H GLN* 3.6 25.8 - - - -
20H ALA 4.3 1.1 - - - -
21H THR* 1.3 78.5 - - - +
23H SER* 1.3 60.4 + - - +
24H LEU 3.8 0.4 - - - -
44H ALA* 3.7 3.6 - - - -
59H GLY* 3.9 4.7 - - - +
62H GLY* 5.5 0.7 - - - -
64H VAL* 3.4 29.8 + - + +
66H CYS* 2.0 54.7 - - + +
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Residues in contact with SER 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H TRP* 3.9 8.3 - - - -
14H LEU 3.8 2.2 + - - -
16H GLN* 3.3 30.1 + - - +
21H THR* 3.8 4.9 + - - -
22H CYS* 1.3 74.1 - - - +
24H LEU* 1.3 74.0 + - - +
25H VAL* 4.1 1.9 + - - +
56H ASN* 5.1 0.9 - - - +
59H GLY* 4.1 23.7 - - - -
60H PHE* 4.6 14.1 - - - -
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Residues in contact with LEU 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E GLY 4.0 27.4 - - - +
2E LEU* 5.4 5.6 - - + -
55E SER* 4.4 28.3 - - - +
56E LEU 4.7 11.0 - - - +
57E SER* 5.6 2.5 - - - +
13H TRP* 3.4 8.9 - - - -
14H LEU* 2.9 43.1 + - + +
16H GLN* 3.5 22.9 - - - +
23H SER* 1.3 92.6 + - - +
25H VAL* 1.3 63.6 + - - +
26H LEU* 3.4 2.4 + - + -
60H PHE* 5.4 3.4 - - + -
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Residues in contact with VAL 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E SER* 3.1 33.4 + - - +
11H VAL* 3.9 19.1 - - + -
12H CYS 3.9 2.9 - - - -
13H TRP* 3.5 31.0 - - + -
23H SER 4.1 1.3 + - - +
24H LEU* 1.3 70.2 - - - +
26H LEU* 1.3 66.0 + - - +
27H GLN 4.2 8.5 - - - +
28H THR* 4.3 15.9 - - + +
55H ILE* 4.2 15.3 - - + -
56H ASN* 4.4 21.5 - - - +
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Residues in contact with LEU 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU* 4.0 22.4 - - + -
55E SER* 5.2 3.7 + - - -
12H CYS* 2.8 26.2 + - + +
13H TRP 4.3 11.9 - - - +
14H LEU* 3.9 40.4 - - + -
24H LEU* 3.4 6.7 + - + +
25H VAL* 1.3 81.1 - - - +
27H GLN* 1.3 60.6 + - + +
40H ASN* 5.8 2.7 - - - +
43H THR* 4.4 13.0 - - - +
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Residues in contact with GLN 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H VAL* 3.6 2.3 - - - +
12H CYS* 2.7 37.5 + - + +
25H VAL* 4.4 3.6 - - - -
26H LEU* 1.3 82.1 - - + +
28H THR* 1.3 62.3 + - - +
30H VAL* 3.5 26.7 - - + +
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Residues in contact with THR 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LYS* 5.1 3.6 - - - -
10H GLY 4.1 3.1 - - - -
11H VAL* 4.3 11.9 - - + +
25H VAL* 4.3 11.0 - - + +
27H GLN* 1.3 77.2 - - - +
29H ASP* 1.3 74.8 + - - +
30H VAL* 3.4 8.7 + - - +
49H THR* 6.2 2.5 - - + -
52H GLY 5.8 0.4 - - - +
55H ILE* 4.2 24.7 - - + -
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Residues in contact with ASP 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C GLY 5.4 4.0 - - - +
143C LYS* 2.8 39.1 + - - +
161C THR* 5.5 9.1 - - + +
9H GLY* 4.7 13.2 - - - +
10H GLY 2.9 18.0 + - - +
11H VAL* 5.1 0.4 - - - +
28H THR* 1.3 79.5 - - - +
30H VAL* 1.3 58.8 - - - +
49H THR* 6.2 1.4 - - - +
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Residues in contact with VAL 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LYS* 5.4 5.4 - - - -
9H GLY* 4.3 2.5 - - - -
10H GLY 2.9 25.2 + - - +
11H VAL 4.1 1.1 - - - -
12H CYS* 3.6 26.0 - - + +
27H GLN* 3.5 35.9 - - + +
28H THR 3.6 7.9 - - - +
29H ASP* 1.3 82.6 - - - +
31H THR* 1.3 63.2 + - - +
34H GLU* 4.1 20.4 - - + +
35H CYS* 4.6 3.6 - - + +
45H TRP* 2.9 15.7 + - + +
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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