Contacts of the strand formed by residues 85 - 89 (chain A) in PDB entry 2HHL
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 GLU 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.7 2.0 - - - +
21A VAL* 4.4 12.0 - - - +
22A THR 5.5 0.3 + - - -
25A ASP* 3.3 32.4 - - + +
28A LYS* 3.9 10.6 - - + +
29A LYS 3.0 14.5 + - - +
30A CYS* 3.2 17.0 - - - +
31A VAL 2.8 30.4 + - - +
84A PHE* 1.3 68.8 - - - +
86A CYS* 1.3 56.2 + - - +
87A VAL* 4.7 6.7 - - + +
111A ARG* 4.1 20.4 - - + +
135A ARG* 2.8 48.7 + - - -
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Residues in contact with CYS 86 (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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31A VAL* 3.4 7.6 - - - +
33A ILE* 4.4 7.4 - - + -
80A MET* 3.3 48.5 - - - -
81A GLY* 3.8 6.5 - - - -
84A PHE* 3.4 12.6 + - - -
85A GLU* 1.3 73.2 - - - +
87A VAL* 1.3 63.9 + - - +
109A VAL* 3.7 17.9 + - + +
110A PHE* 3.5 19.0 - - + -
111A ARG* 2.9 32.0 + - - +
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Residues in contact with VAL 87 (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 LEU* 4.1 22.4 - - + -
30A CYS* 3.9 21.1 - - - -
31A VAL 2.8 11.7 + - - +
32A VAL* 3.4 17.3 - - + -
33A ILE* 2.6 33.4 + - - -
85A GLU* 4.4 9.2 - - + +
86A CYS* 1.3 81.1 - - - +
88A LEU* 1.3 67.7 + - - +
89A PHE* 4.7 1.6 - - + -
110A PHE* 3.8 2.9 - - - -
111A ARG* 5.1 0.9 - - + -
112A ALA* 3.5 13.7 - - + +
114A LEU* 3.8 28.7 - - + -
133A LEU* 4.8 0.9 - - + -
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Residues in contact with LEU 88 (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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33A ILE 3.4 15.3 - - - +
34A ASP 4.2 4.9 - - - +
35A LEU* 4.0 34.3 - - + -
39A LEU* 4.3 1.1 - - + -
87A VAL* 1.3 73.5 - - - +
89A PHE* 1.3 55.6 + - - +
90A THR* 4.8 7.2 - - + -
97A ALA 4.9 2.5 - - - +
101A ALA* 3.7 30.3 - - + -
110A PHE* 3.4 36.1 - - + -
112A ALA 3.0 12.7 + - - +
113A ARG* 3.3 17.4 - - + -
114A LEU* 2.7 33.4 + - - +
115A PHE* 4.4 11.7 - - + -
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Residues in contact with PHE 89 (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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17A LEU* 3.9 15.5 - - + -
32A VAL* 3.5 33.6 - - + +
33A ILE 2.9 7.2 + - - -
34A ASP* 3.5 13.9 - - - -
87A VAL* 3.6 2.2 + - + +
88A LEU* 1.3 75.1 - - - +
90A THR* 1.3 65.5 + - - +
114A LEU* 3.3 28.0 - - + -
115A PHE 4.4 0.2 - - - -
118A SER* 3.3 41.5 - - - -
119A CYS* 3.6 18.2 - - - -
128A LYS* 2.9 52.1 + - + -
129A ASP 4.7 0.7 - - - -
130A LEU* 5.0 3.6 - - + -
133A LEU* 4.2 11.9 - - + -
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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