Contacts of the strand formed by residues 26 - 31 (chain A) in PDB entry 4H27
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 SER 26 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP* 4.9 4.4 + - - -
20A SER* 3.5 8.8 + - - -
25A THR* 1.3 74.6 + - - +
27A VAL* 1.3 59.5 + - - +
28A TYR* 3.8 32.5 + - - -
296A PRO 4.1 6.7 + - - -
297A SER* 3.3 8.4 - - - -
298A LEU 2.8 27.9 + - - +
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG 3.6 0.7 - - - +
15A ASP* 3.8 3.5 + - - +
16A SER* 3.0 27.7 + - - -
19A LEU* 3.6 46.2 - - + +
20A SER* 2.9 11.9 + - - +
23A ALA* 3.7 14.6 - - + -
25A THR* 3.7 10.8 - - + +
26A SER* 1.3 75.6 - - - +
28A TYR* 1.3 62.6 + - - +
29A LEU* 4.0 21.3 - - + -
277A VAL* 4.3 7.6 - - + -
298A LEU* 3.4 7.9 - - + +
300A VAL* 4.1 17.7 - - + -
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.7 20.2 - - + -
14A ARG 3.4 2.2 - - - -
15A ASP* 3.7 36.5 + - + -
26A SER* 3.8 19.9 + - - -
27A VAL* 1.3 75.5 - - - +
29A LEU* 1.3 63.2 + - - +
30A LYS 3.7 0.7 + - - -
156A LEU* 3.9 23.3 - - + -
158A GLU* 6.1 5.2 - - + +
297A SER* 3.7 32.5 - - - -
298A LEU 2.8 12.9 + - - +
299A VAL* 3.2 18.1 - - + +
300A VAL 2.9 25.6 + - - +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PRO 3.7 0.2 - - - +
13A ILE* 3.2 7.0 - - - -
14A ARG* 2.8 46.1 + - + +
16A SER* 4.0 23.8 - - - -
19A LEU* 3.8 19.7 - - + -
27A VAL* 4.0 6.7 - - + -
28A TYR* 1.3 70.5 - - - +
30A LYS* 1.3 61.6 + - - +
31A MET* 3.5 18.1 + - - +
258A PHE* 3.8 23.1 - - + -
262A GLU* 4.0 15.9 - - + -
274A LEU* 4.2 7.0 - - + -
300A VAL* 3.7 24.5 - - + -
302A VAL* 4.0 11.0 - - + -
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 5.5 0.2 - - - +
11A THR* 2.8 35.0 + - - +
12A PRO 3.8 5.6 - - - +
13A ILE* 4.1 10.2 - - + +
28A TYR 3.7 1.6 + - - -
29A LEU* 1.3 68.8 - - - +
31A MET* 1.3 60.7 + - - +
32A ASP* 3.0 7.0 + - - +
43A ARG* 3.8 7.0 - - - +
148A ILE* 3.8 32.3 - - + -
151A GLU* 2.7 43.5 + - - +
152A LEU* 4.0 15.9 - - + -
155A THR* 5.7 1.4 + - - -
299A VAL* 4.2 9.6 - - + -
300A VAL 2.9 15.7 + - - +
301A ILE* 3.9 11.8 - - + -
302A VAL* 2.9 28.1 + - - +
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Residues in contact with MET 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR* 3.3 16.5 - - - -
12A PRO* 2.9 36.1 + - + +
14A ARG* 3.8 38.4 - - + +
29A LEU* 3.6 33.2 - - - +
30A LYS* 1.3 69.0 - - - +
32A ASP* 1.3 57.1 + - - +
33A SER* 3.1 24.0 - - - +
34A ALA* 3.0 21.0 + - + +
258A PHE* 4.3 13.0 - - + -
264A ILE* 3.8 24.5 - - + -
302A VAL* 4.1 9.0 - - + -
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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