Contacts of the strand formed by residues 88 - 92 (chain A) 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 LYS 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLY 3.5 5.4 - - - -
72A ILE* 4.3 13.5 - - + +
86A GLY 3.5 4.0 + - - +
87A ASP* 1.3 74.2 - - - +
89A VAL* 1.3 65.5 + - - +
159A LYS* 3.4 4.8 - - - +
160A ILE* 3.0 42.6 + - + +
161A ASP 3.9 8.3 - - - +
162A ALA* 3.0 33.0 + - + +
163A ALA* 4.3 1.6 - - - +
164A SER 2.9 21.5 + - - +
166A LEU* 3.7 34.4 - - + +
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Residues in contact with VAL 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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38A ILE* 3.8 18.6 - - + -
70A ALA* 3.4 4.2 - - - +
71A GLY 2.9 37.5 + - - +
73A VAL* 3.6 33.4 - - + -
83A VAL* 4.0 13.2 - - + -
87A ASP* 4.1 1.6 - - + +
88A LYS* 1.3 80.0 - - - +
90A ILE* 1.3 64.5 + - - +
91A PRO* 3.8 1.3 - - + +
157A VAL* 3.8 22.4 - - + -
158A ALA 3.0 16.4 - - - +
159A LYS* 3.7 10.1 - - + -
160A ILE* 4.1 3.5 - - - +
166A LEU* 5.4 0.2 - - - +
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Residues in contact with ILE 90 (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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69A ALA 3.3 18.2 - - - +
70A ALA* 4.4 2.5 - - + -
89A VAL* 1.3 74.6 - - - +
91A PRO* 1.3 68.5 - - - +
92A LEU* 3.5 3.9 + - + +
157A VAL* 4.3 1.8 - - - -
158A ALA* 2.8 35.8 + - + +
160A ILE* 3.6 17.3 - - + -
169A VAL* 3.5 38.1 - - + +
172A ILE* 4.3 3.1 - - + -
173A GLY* 3.5 25.6 - - - -
328A ILE* 3.6 31.0 - - + -
332A VAL* 3.8 12.8 - - + -
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Residues in contact with PRO 91 (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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38A ILE* 4.5 8.7 - - + -
40A MET* 4.6 8.5 - - + -
67A HIS 3.6 14.1 - - - +
69A ALA* 3.0 24.2 - - + +
70A ALA* 4.4 0.9 - - - +
89A VAL* 3.8 7.6 - - + +
90A ILE* 1.3 91.6 - - - +
92A LEU* 1.3 62.3 + - - +
93A PHE 3.8 0.3 + - - -
143A THR* 4.3 14.0 - - + +
145A THR* 3.5 29.2 - - + -
152A VAL* 4.4 16.2 - - + -
156A ALA 3.7 6.3 - - - +
157A VAL* 4.2 4.0 - - + -
173A GLY 4.4 0.9 - - - +
319A TYR* 4.3 1.7 + - - -
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Residues in contact with LEU 92 (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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90A ILE* 4.0 8.3 - - + +
91A PRO* 1.3 72.7 - - - +
93A PHE* 1.3 59.1 + - - +
94A THR 3.0 17.9 + - - +
141A LEU 4.6 0.5 - - - +
143A THR* 3.7 9.0 - - - +
155A ASN 3.9 4.0 - - - +
156A ALA* 2.8 29.5 + - - +
157A VAL 3.7 22.4 - - - +
158A ALA* 4.1 7.4 - - + -
319A TYR* 3.2 18.4 - - - +
324A SER* 3.5 11.9 - - - +
325A LYS* 3.5 35.9 - - + +
328A ILE* 3.5 30.3 - - + -
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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