Contacts of the strand formed by residues 143 - 147 (chain R) in PDB entry 3HOU
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 PHE 143 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70R LYS* 4.5 12.8 - - + -
72R LYS* 3.0 46.0 + - + -
73R ALA* 3.7 21.5 - - + -
74R ILE* 3.1 23.5 + - - +
135R ARG* 3.2 54.5 - - + -
136R ARG 2.9 17.7 - - - +
137R TYR* 3.8 17.5 - + + -
138R LEU* 4.6 1.1 - - - +
141R GLY 4.0 7.0 - - - -
142R SER* 1.3 81.2 - - - +
144R GLU* 1.3 61.3 + - - +
145R ASP* 3.3 16.6 - - - -
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Residues in contact with GLU 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R ILE* 3.6 33.5 - - + +
78R GLN 3.9 0.9 - - - +
79R ARG* 3.2 20.5 - - + +
80R ALA* 3.0 21.7 + - - +
81R THR* 2.3 55.5 + - + +
136R ARG* 2.9 33.5 + - + +
138R LEU* 4.5 8.1 - - + -
143R PHE* 1.3 76.5 - - - +
145R ASP* 1.3 63.4 + - - +
146R TRP* 3.5 16.9 - - - +
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Residues in contact with ASP 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R ILE 5.1 2.4 + - - -
76R LYS* 3.9 13.0 + - + +
79R ARG* 3.1 26.4 + - - +
133R VAL* 3.7 9.9 - - + -
134R ILE 3.6 2.2 - - - -
135R ARG* 2.7 59.9 + - - +
143R PHE* 3.3 10.1 + - - -
144R GLU* 1.3 69.8 - - - +
146R TRP* 1.3 62.7 + - - +
58S ARG* 2.9 29.6 + - - +
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Residues in contact with TRP 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76R LYS* 5.5 0.2 - - - -
79R ARG* 3.6 32.5 - - + +
81R THR* 2.9 36.8 + - - -
82R THR 3.7 11.0 - - - -
83R PRO* 3.7 27.8 - - + -
133R VAL* 3.4 4.8 - - - -
134R ILE* 2.7 42.4 + - + +
136R ARG* 3.6 15.8 - - + +
144R GLU* 3.5 23.7 - - - +
145R ASP* 1.3 79.9 - - - +
147R SER* 1.3 59.9 + - - +
150R GLU* 3.6 28.5 - - + -
151R LEU* 3.5 35.6 - - + +
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Residues in contact with SER 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1446M ASP* 5.8 2.2 - - - -
1449M SER* 6.1 2.2 - - - -
76R LYS* 5.2 3.3 - - - +
132R LEU 3.8 9.0 - - - -
133R VAL* 4.2 11.6 - - - +
146R TRP* 1.3 73.6 - - - +
148R VAL* 1.3 64.9 + - - +
149R GLU* 3.3 12.6 - - - +
150R GLU* 2.9 42.2 + - - +
151R LEU* 3.0 22.5 + - - +
58S ARG* 6.1 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