Contacts of the strand formed by residues 15 - 20 (chain A) in PDB entry 2PH6
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 TYR 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ASN 4.0 0.5 - - - +
6A LEU* 3.4 8.6 - - - +
7A ARG* 2.9 69.3 + - + +
8A GLY* 4.1 7.7 + - - -
13A GLY 3.6 11.2 - - - -
14A TYR* 1.3 74.9 - - - +
16A VAL* 1.3 61.4 + - - +
17A GLU* 5.3 0.9 - - + -
28A ASN* 3.5 34.8 - - + -
29A ILE 3.0 24.5 - - - +
30A LEU* 3.9 0.7 - - - +
113A SER 3.5 22.9 - - - -
114A ASN* 3.1 27.2 + - + +
115A TRP* 3.9 17.9 - - + -
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Residues in contact with VAL 16 (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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5A ASN* 3.7 31.0 - - + +
6A LEU* 3.6 16.8 - - + -
15A TYR* 1.3 76.1 - - - +
17A GLU* 1.3 64.7 + - - +
18A MET* 4.0 21.8 - - + -
28A ASN* 4.6 1.3 - - - -
29A ILE* 2.8 34.9 + - + +
31A VAL* 3.9 15.9 - - + +
87A ILE* 3.9 24.0 - - + -
89A HIS* 5.6 2.2 - - + +
119A LEU* 4.8 7.9 - - + -
174A MET* 4.9 7.0 - - - -
176A ILE* 6.2 0.4 - - + -
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Residues in contact with GLU 17 (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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5A ASN 4.6 3.1 + - - +
15A TYR* 5.9 0.7 - - + -
16A VAL* 1.3 75.0 - - - +
18A MET* 1.3 59.2 - - - +
26A THR* 4.0 22.9 - - + +
27A LEU 3.5 5.2 - - - -
28A ASN* 3.6 22.6 + - - +
50A ARG* 4.6 4.3 + - - -
87A ILE* 3.3 25.3 - - - +
88A PRO* 3.5 15.5 - - + +
89A HIS* 3.4 30.4 + - + -
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Residues in contact with MET 18 (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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16A VAL* 4.0 10.8 - - + -
17A GLU* 1.3 80.1 - - - +
19A THR* 1.3 62.2 + - - +
20A VAL* 4.0 4.0 + - + +
25A GLN 3.7 1.7 - - - +
26A THR* 3.4 1.3 - - - -
27A LEU* 3.0 32.8 + - - +
29A ILE* 3.7 29.8 - - + -
38A PHE* 3.7 31.2 - - + -
85A VAL* 3.6 27.8 - - + -
86A SER 3.4 6.3 - - - +
87A ILE* 4.0 16.2 - - + -
88A PRO* 4.2 0.4 - - - -
119A LEU* 4.0 21.5 - - + -
136A PHE* 4.0 16.8 - - + -
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Residues in contact with THR 19 (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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18A MET* 1.3 74.3 - - - +
20A VAL* 1.3 63.5 + - - +
21A GLY 4.4 1.3 + - - +
24A PRO* 3.5 35.2 - - + -
25A GLN 3.5 3.6 - - - +
26A THR* 2.9 22.9 + - - +
84A LEU 3.8 0.5 - - - +
85A VAL* 3.3 4.7 - - - -
86A SER* 2.7 50.1 + - - +
88A PRO* 3.6 16.9 - - - +
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Residues in contact with VAL 20 (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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18A MET* 4.5 6.5 - - + +
19A THR* 1.3 82.2 - - - +
21A GLY* 1.3 64.6 + - - +
25A GLN* 2.8 45.3 + - - +
27A LEU* 5.2 7.4 - - + -
29A ILE* 6.2 0.4 - - + -
38A PHE* 4.1 25.8 - - + -
40A VAL* 5.1 8.1 - - + -
52A TYR* 3.6 31.0 - - + +
83A ASP* 4.1 0.4 - - - +
84A LEU 3.4 5.4 - - - +
85A VAL* 4.5 5.2 - - + -
99A ILE* 3.5 29.8 - - + -
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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