Contacts of the strand formed by residues 25 - 32 (chain H) in PDB entry 5IYB
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 25 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A ARG* 3.1 46.7 - - + +
552A ASP* 3.9 6.3 - - + -
554A PHE* 3.6 25.1 - - + -
22H PHE* 3.9 12.6 + - + +
23H ASP* 2.3 40.7 + - - +
24H ARG* 1.3 69.1 - - - +
26H SER* 1.3 65.6 + - - +
42H ASP* 3.8 27.4 - - + +
43H VAL 3.3 11.2 - - - +
44H ASN* 5.1 0.2 - - - -
121H LEU* 4.4 10.8 - - + -
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Residues in contact with SER 26 (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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551A ARG* 6.1 0.4 - - - +
15H ILE* 3.9 22.4 + - - +
21H LYS* 5.6 7.1 - - - +
22H PHE* 5.8 3.4 - - - +
25H VAL* 1.3 78.6 - - - +
27H ARG* 1.3 62.2 + - - +
28H LEU* 5.2 0.7 - - - -
42H ASP* 3.4 5.0 - - - -
43H VAL* 3.0 33.2 + - - +
45H ILE* 3.6 33.8 - - - +
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Residues in contact with ARG 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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551A ARG* 3.9 17.2 - - - +
622A SER* 3.5 33.3 + - - -
623A PRO* 5.0 4.7 - - - +
625A ASP* 4.0 23.3 + - - +
15H ILE 2.8 26.7 + - - +
17H PRO* 3.4 28.2 - - + +
18H GLU* 4.8 11.1 + - - -
26H SER* 1.3 75.2 + - - +
28H LEU* 1.3 64.7 + - - +
29H HIS* 4.2 9.2 - - + -
40H ILE* 3.7 30.9 - - + +
41H LEU 3.6 5.4 - - - +
42H ASP* 3.2 30.6 + - - +
122H LEU* 4.8 10.3 - - - +
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Residues in contact with LEU 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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12H VAL* 5.1 4.7 - - + -
14H ASP 3.7 2.2 - - - +
15H ILE* 3.7 35.4 - - + -
26H SER 4.9 0.9 - - - +
27H ARG* 1.3 75.3 - - - +
29H HIS* 1.3 70.7 + - - +
30H CYS* 3.9 15.0 - - - -
40H ILE* 3.5 3.5 - - - +
41H LEU* 2.7 41.0 + - + +
43H VAL* 3.8 38.1 - - + -
45H ILE* 5.0 2.5 - - + -
50H VAL* 4.5 23.3 - - + -
56H PHE* 4.4 21.8 - - + -
145H MET* 4.9 4.3 - - + -
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Residues in contact with HIS 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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622A SER* 5.9 3.5 + - - -
12H VAL* 3.6 1.0 - - - -
13H LYS* 2.6 42.1 + - + +
14H ASP* 2.7 33.4 + - + +
17H PRO* 3.3 39.2 - - + +
27H ARG* 4.2 5.6 - - - -
28H LEU* 1.3 81.2 + - - +
30H CYS* 1.3 56.4 + - - +
39H LEU 3.9 1.6 - - - -
40H ILE* 3.4 40.6 - - + +
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Residues in contact with CYS 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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10H PHE* 4.6 6.1 - - + -
11H ASP 3.1 13.5 - - - +
12H VAL* 4.2 5.6 - - - -
13H LYS* 4.0 6.2 - - - +
28H LEU* 3.9 18.6 - - - -
29H HIS* 1.3 80.3 - - - +
31H GLU* 1.3 62.1 + - - +
38H ASP* 3.6 11.1 - - - +
39H LEU* 2.7 52.2 + - + +
56H PHE* 3.7 36.1 - - + -
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Residues in contact with GLU 31 (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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10H PHE* 4.6 3.1 - - - -
11H ASP* 2.8 50.3 + - + +
12H VAL 5.6 0.2 - - - +
13H LYS* 2.7 45.3 + - + +
30H CYS* 1.3 74.2 - - - +
32H SER* 1.3 65.9 + - - +
35H PHE* 6.3 0.4 - - - -
37H MET 4.0 7.6 - - - +
38H ASP* 4.5 4.3 - - + +
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Residues in contact with SER 32 (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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8H ASP* 3.5 6.3 - - - -
10H PHE* 3.3 33.6 - - - -
11H ASP* 5.7 0.2 - - - -
31H GLU* 1.3 78.1 - - - +
33H GLU* 1.3 59.9 + - - +
34H SER* 3.7 4.6 + - - -
35H PHE* 2.9 22.2 + - - +
36H LYS 3.3 6.8 + - - -
37H MET* 2.6 50.3 + - - +
38H ASP* 4.7 0.4 - - - +
39H LEU* 6.3 0.2 - - - +
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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