Contacts of the strand formed by residues 68 - 72 (chain B) in PDB entry 1HDZ
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 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B VAL* 3.4 5.2 - - - +
44B GLY* 3.1 44.6 + - - +
46B CYS* 4.1 5.6 - - + +
49B ASP* 5.3 0.2 + - - -
67B HIS* 1.3 81.7 - - + +
69B ALA* 1.3 63.0 + - - +
145B THR* 3.9 2.9 + - - -
170B CYS 3.3 17.7 - - - +
171B LEU* 3.0 22.7 - - - +
173B GLY 4.8 1.6 - - - -
174B CYS* 3.8 15.7 - - + +
175B GLY* 2.9 26.4 + - - -
369B ARG* 2.7 35.7 + - - -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET* 3.9 10.8 - - - -
42B ALA 3.3 13.5 - - - +
43B VAL* 4.1 0.9 - - + -
67B HIS 3.7 3.2 + - - -
68B GLU* 1.3 76.0 - - - +
70B ALA* 1.3 63.4 + - - +
90B ILE* 3.3 19.1 - - - +
91B PRO* 3.2 20.1 - - + +
145B THR* 3.7 31.4 - - + -
170B CYS* 3.6 16.3 + - - +
173B GLY* 4.7 2.8 - - - -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET* 4.0 6.2 - - - +
41B VAL 3.1 17.5 + - - -
42B ALA 3.1 14.1 + - - +
69B ALA* 1.3 78.5 - - - +
71B GLY* 1.3 57.7 + - - +
89B VAL 3.3 9.9 - - - +
90B ILE* 4.3 7.2 - - + -
166B LEU* 3.5 47.8 - - + +
169B VAL* 5.0 1.1 - - + -
170B CYS* 3.6 9.8 - - + +
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Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.9 10.9 - - - +
39B LYS 3.1 14.8 - - - -
40B MET* 4.4 0.9 - - - +
41B VAL* 3.8 7.9 - - - -
70B ALA* 1.3 76.0 - - - +
72B ILE* 1.3 65.4 + - - -
88B LYS* 3.6 4.3 - - - -
89B VAL 2.8 30.7 + - - -
166B LEU* 3.7 8.9 - - - +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.2 4.8 - - - +
39B LYS* 2.9 42.2 + - + +
41B VAL* 3.7 22.0 - - + -
71B GLY* 1.3 78.0 - - - +
73B VAL* 1.3 69.1 + - - +
74B GLU 3.3 0.3 + - - -
86B GLY* 3.5 32.1 - - - +
87B ASP 3.6 2.9 - - - -
88B LYS* 4.7 9.2 - - + -
166B LEU* 4.4 8.1 - - + -
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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