Contacts of the strand formed by residues 129 - 133 (chain E) in PDB entry 3PHW
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 ALA 129 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E VAL* 4.8 0.2 - - + -
19E SER 3.2 8.7 - - - +
20E ASN* 3.3 5.4 - - - +
21E PRO* 4.8 0.4 - - - -
119E TRP* 3.7 1.8 - - - -
120E THR* 3.1 30.0 + - + +
127E VAL* 3.5 14.4 - - - +
128E GLU* 1.3 84.5 - - + +
130E GLY* 1.3 59.3 + - - +
131E ILE* 5.7 0.4 - - - -
8F LEU* 3.2 46.9 - - + +
9F THR* 4.3 0.9 - - - -
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Residues in contact with GLY 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TRP* 3.7 8.7 - - - -
18E VAL* 3.3 9.4 - - - +
19E SER 2.9 30.8 + - - +
117E ILE* 4.9 0.2 - - - -
118E ILE 3.4 9.2 - - - -
119E TRP* 3.7 22.0 - - - -
129E ALA* 1.3 75.1 - - - +
131E ILE* 1.3 63.2 + - - -
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Residues in contact with ILE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TRP* 4.2 0.9 - - - -
12E VAL* 6.3 0.4 - - + -
16E GLN* 5.3 4.5 - - + +
17E TYR 3.2 11.0 - - - +
18E VAL* 4.4 5.8 - - + -
102E THR* 4.4 5.6 - - + -
116E ILE 3.8 1.2 - - - +
117E ILE* 3.4 2.4 - - - -
118E ILE* 2.9 35.9 + - + +
120E THR* 6.5 0.4 - - + -
129E ALA 5.7 0.2 - - - -
130E GLY* 1.3 77.6 - - - +
132E LYS* 1.3 63.7 + - - +
133E PHE* 3.8 29.7 - - + -
8F LEU* 3.6 31.6 - - + -
42F ARG* 6.0 0.2 - - - +
70F VAL* 4.1 12.6 - - + -
71F LEU 3.9 16.6 - - - +
73F LEU* 3.8 28.3 - - + -
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Residues in contact with LYS 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E TRP* 3.6 49.8 - - + +
16E GLN* 3.3 6.2 - - - +
17E TYR* 2.7 56.7 + - + -
115E THR* 3.5 18.8 - - + -
116E ILE 3.5 2.9 - - - -
117E ILE* 3.6 22.0 - - + -
131E ILE* 1.3 72.5 - - - +
133E PHE* 1.3 62.3 + - - +
134E GLY 2.8 22.6 + - - +
135E ASP* 3.4 11.7 + - - +
136E GLY 2.8 28.2 + - - +
137E ASP* 5.0 0.9 - - - -
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Residues in contact with PHE 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLY 3.5 5.8 - - - +
16E GLN* 3.6 35.7 - - + -
78E GLU* 5.1 0.4 - - - -
102E THR* 3.5 48.2 - - + -
105E ALA* 4.0 20.4 - - + +
106E SER* 3.6 20.9 - - - -
109E ALA* 3.7 22.1 - - + +
115E THR* 3.2 4.5 - - - +
116E ILE* 2.8 42.8 + - + +
118E ILE* 4.1 6.5 - - + -
131E ILE* 3.8 27.4 - - + -
132E LYS* 1.3 73.1 - - - +
134E GLY* 1.3 58.3 + - - +
42F ARG* 5.1 3.4 - - - -
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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