Contacts of the strand formed by residues 7 - 11 (chain I) in PDB entry 3AOH
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 LYS 7 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102H LEU* 2.7 49.4 + - + +
1103H ASP 4.2 3.6 - - - +
1104H GLU 3.3 20.5 + - - -
1105H LYS* 5.3 0.6 - - - +
1106H ASP* 2.6 38.6 + - - +
5I VAL* 3.7 1.5 - - - +
6I ARG* 1.3 92.1 - - + +
8I VAL* 1.3 62.4 + - - +
1456I LYS* 5.3 11.4 - - + -
1457I ASP 4.3 2.0 - - - +
1458I GLU* 3.4 30.2 + - - +
1459I LEU* 4.2 2.5 - - - -
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Residues in contact with VAL 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085H PHE* 4.7 20.0 - - + -
1099H VAL* 4.3 14.8 - - + -
1100H GLN 3.7 7.9 - - - +
1101H THR* 5.1 5.8 - - + -
5I VAL* 5.1 5.2 - - + -
7I LYS* 1.3 79.7 - - - +
9I ARG* 1.3 60.3 + - - +
1434I TRP* 2.9 27.5 - - + -
1435I LEU* 5.2 5.6 - - + -
1456I LYS* 3.3 4.3 - - - -
1457I ASP* 2.9 33.9 + - + +
1459I LEU* 3.3 36.1 - - + -
1468I LEU* 4.9 4.5 - - + -
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Residues in contact with ARG 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098H ASP 2.8 9.6 - - - +
1099H VAL* 3.1 2.3 - - - -
1100H GLN* 2.5 81.2 + - + +
1102H LEU* 3.8 12.7 - - + +
8I VAL* 1.3 73.7 - - - +
10I ILE* 1.3 65.3 + - - +
11I ALA* 3.4 20.4 - - - +
17I LYS* 4.8 4.4 - - - +
505I SER* 4.7 9.3 + - - -
507I ASN* 3.3 31.7 + - - +
1434I TRP* 4.0 0.9 - - - -
1454I GLY* 4.5 13.2 - - - +
1455I LYS 3.7 3.8 - - - +
1456I LYS* 3.6 39.4 - - + +
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Residues in contact with ILE 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092H LEU* 4.8 6.5 - - + -
1097H LEU* 3.1 43.5 - - + -
1098H ASP 3.4 2.0 - - - -
1099H VAL* 3.7 15.5 - - + -
9I ARG* 1.3 73.9 - - - +
11I ALA* 1.3 59.8 + - - +
1434I TRP* 3.3 47.3 - - + +
1447I LEU* 5.2 6.3 - - + +
1450I ALA* 3.3 24.7 - - + +
1451I ALA* 3.5 5.3 - - - +
1454I GLY* 3.1 23.9 - - - -
1455I LYS 3.2 11.6 + - - +
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Residues in contact with ALA 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097H LEU* 3.0 6.3 - - - -
1098H ASP* 2.3 51.2 + - - +
1100H GLN* 4.4 1.8 - - - +
9I ARG* 3.4 24.2 - - - +
10I ILE* 1.3 75.8 - - - +
12I LEU* 1.3 66.2 + - + +
505I SER* 6.2 0.2 - - - -
507I ASN* 3.3 28.3 - - + +
1451I ALA 4.4 0.7 - - - -
1454I GLY* 4.6 3.6 - - - -
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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
------------------------------------------------------------
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