Contacts of the strand formed by residues 127 - 131 (chain C) in PDB entry 1SOZ
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 LEU 127 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ILE* 3.8 18.8 - - + -
93C THR 3.4 13.2 - - - +
94C ASN* 4.5 5.2 - - - +
95C LYS* 3.5 4.4 - - - +
121C SER* 3.4 0.7 - - - -
122C ASP 3.0 26.0 + - - -
125C THR* 3.0 25.1 - - - +
126C ASP* 1.3 79.1 - - - +
128C ALA* 1.3 65.8 + - - +
215C ILE* 4.5 7.4 - - + -
236C ILE* 3.9 24.2 - - + -
241C ALA* 3.5 33.9 - - + +
244C ILE* 3.6 31.2 - - + -
245C MET* 5.2 0.7 - - - +
248C LEU* 4.7 1.6 - - + -
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Residues in contact with ALA 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ILE 3.6 1.0 - - - +
92C ILE* 3.5 4.2 - - - +
93C THR* 2.7 44.1 + - + +
94C ASN 4.0 0.9 - - - +
95C LYS* 3.8 16.6 - - - +
98C ILE* 4.0 20.2 - - + -
118C LEU* 4.8 1.8 - - + -
120C GLY 3.5 11.7 - - - +
121C SER* 4.0 5.8 - - - +
127C LEU* 1.3 81.9 - - - +
129C VAL* 1.3 65.2 + - - +
248C LEU* 4.2 2.0 - - - +
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 3.8 24.7 - - + -
91C ILE 3.4 9.4 - - - +
92C ILE* 5.0 4.0 - - + -
118C LEU* 3.7 0.7 - - - +
119C VAL* 3.0 36.6 + - + -
120C GLY 3.0 12.1 + - - +
127C LEU* 6.4 0.2 - - + -
128C ALA* 1.3 75.3 - - - +
130C LEU* 1.3 82.9 + - - +
245C MET* 3.8 29.6 - - + +
248C LEU* 3.5 28.5 - - + -
249C ILE* 4.3 5.2 - - + -
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Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL* 4.6 5.8 - - + -
90C TYR* 3.3 6.1 - - - -
91C ILE* 3.0 46.4 + - + +
93C THR* 4.3 18.8 - - + -
98C ILE* 4.5 9.9 - - + -
104C ILE* 3.8 46.9 - - + -
106C VAL* 4.1 16.8 - - + -
116C ALA* 4.3 5.8 - - + -
117C LEU 3.1 10.5 - - - +
118C LEU* 3.9 16.8 - - + -
119C VAL* 3.5 2.5 - - - -
129C VAL* 1.3 89.7 - - - +
131C LYS* 1.3 63.2 + - - +
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG* 3.2 24.4 + - - +
89C GLY 3.3 11.2 - - - +
90C TYR* 3.4 37.3 + - + +
115C GLU 4.4 0.7 - - - +
116C ALA* 3.8 0.9 - - - -
117C LEU* 3.0 47.5 + - + +
119C VAL* 3.8 13.0 - - + -
130C LEU* 1.3 77.0 - - - +
132C ILE* 1.3 71.9 + - - +
133C ASN* 4.1 19.1 + - - +
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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