Contacts of the strand formed by residues 91 - 97 (chain N) 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 SER 91 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68N THR* 3.5 22.7 - - - -
90N ILE* 1.3 73.6 - - - +
92N PHE* 1.3 67.5 + - - +
93N GLY 4.1 0.4 - - - -
131N ASP 4.4 0.2 - - - -
132N VAL* 3.4 6.4 - - - +
133N LYS* 2.9 57.3 + - - +
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Residues in contact with PHE 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N ILE* 4.0 15.7 - - + +
64N CYS* 3.7 17.8 - - - -
67N SER* 3.5 44.1 - - - -
68N THR* 4.7 2.2 - - - +
69N LEU* 4.7 6.3 - - + -
90N ILE* 3.8 21.5 - - + -
91N SER* 1.3 77.7 - - - +
93N GLY* 1.3 65.0 + - - +
130N VAL* 3.8 15.7 - - + -
131N ASP 3.8 3.4 - - - -
132N VAL* 4.0 28.7 - - + -
167N ILE* 6.2 4.0 - - + -
421N PHE* 4.6 12.1 - + - -
424N LEU* 6.1 0.9 - - + -
425N THR* 4.6 5.6 - - - -
428N ILE* 3.5 33.0 - - + -
448N ILE* 6.5 0.9 - - + -
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Residues in contact with GLY 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N GLN* 3.7 9.1 + - - -
63N ILE* 4.2 1.6 - - - +
64N CYS* 5.0 2.5 - - - -
91N SER 4.1 0.6 - - - -
92N PHE* 1.3 73.7 - - - +
94N LYS* 1.3 72.0 + - - +
95N ILE 3.5 0.2 + - - -
130N VAL* 2.9 13.1 - - - +
131N ASP* 3.0 17.8 + - - -
133N LYS* 3.7 24.6 - - - +
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Residues in contact with LYS 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N GLN* 3.5 20.8 - - - +
93N GLY* 1.3 77.9 - - - +
95N ILE* 1.3 67.2 + - - +
96N TYR* 3.2 35.5 + - + +
130N VAL* 3.4 1.2 - - - +
131N ASP* 3.2 36.9 + - - +
133N LYS* 5.0 1.0 - - - +
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Residues in contact with ILE 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N VAL 5.9 1.1 - - - +
59N LEU* 3.8 35.7 - - + -
60N GLN* 3.3 39.1 + - + +
63N ILE* 4.4 14.1 - - + -
94N LYS* 1.3 84.0 - - - +
96N TYR* 1.3 79.2 + - - +
97N VAL* 4.3 1.6 + - + -
128N LEU* 4.4 13.5 - - + -
129N PHE 3.2 6.3 - - - +
130N VAL* 3.0 28.0 - - + -
417N PHE* 5.1 1.8 - - + -
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Residues in contact with TYR 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94N LYS* 3.2 46.6 + - + +
95N ILE* 1.3 76.3 - - - +
97N VAL* 1.3 62.9 + - - +
98N THR* 5.8 0.7 - - + -
127N GLY 3.3 4.9 - - - +
128N LEU* 3.6 2.3 - - - -
129N PHE* 2.3 82.1 + - + +
131N ASP* 2.8 43.4 + - - -
164N LYS 4.2 7.6 - - - -
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Residues in contact with VAL 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N VAL* 4.1 24.5 - - + -
59N LEU* 4.3 15.9 - - + -
95N ILE* 4.3 2.2 + - + -
96N TYR* 1.3 71.4 - - - +
98N THR* 1.3 61.5 + - - +
99N LYS 4.1 0.3 + - - -
126N SER* 5.0 3.4 - - - +
127N GLY 3.5 1.3 - - - +
128N LEU* 3.4 30.3 - - + -
170N LEU* 4.6 6.3 - - + -
178N ASN* 3.0 35.4 - - - +
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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