Contacts of the strand formed by residues 123 - 130 (chain C) in PDB entry 6J8H
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 GLY 123 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C TYR* 4.2 1.8 - - - -
70C GLN 3.3 11.0 - - - -
71C GLU 4.1 9.0 - - - -
72C CYS* 5.5 0.4 - - - -
121C ASP 3.3 2.0 + - - -
122C GLU* 1.3 76.6 - - - +
124C ILE* 1.3 68.3 + - - -
125C TYR* 4.1 4.5 - - - -
142C ILE 3.7 0.3 - - - +
143C HIS* 3.4 7.6 - - - -
144C LEU* 2.9 34.6 + - - +
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Residues in contact with ILE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C THR 3.8 0.3 - - - +
69C TYR* 3.4 4.2 - - - -
70C GLN* 2.8 53.3 + - + +
72C CYS* 4.3 24.5 - - - +
73C ASN* 4.5 19.3 - - - +
123C GLY* 1.3 74.8 - - - -
125C TYR* 1.3 63.4 + - - +
126C ASN* 4.2 2.2 + - - +
141C LYS* 3.3 44.6 - - + -
142C ILE 3.4 2.9 - - - +
143C HIS* 3.5 36.1 - - + +
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Residues in contact with TYR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 3.4 32.1 - - + -
67C TRP* 4.0 8.1 - - + -
68C THR 3.3 3.4 - - - -
69C TYR* 3.2 28.9 - + + -
80C PHE* 3.7 24.5 - + - -
95C PHE* 3.5 25.0 - + - -
114C LEU* 3.5 16.3 - - + +
121C ASP 2.7 30.0 + - - -
123C GLY 3.9 3.8 - - - -
124C ILE* 1.3 75.6 - - - +
126C ASN* 1.3 61.4 + - - +
127C CYS 4.3 0.3 + - - -
140C GLY 3.8 0.5 - - - +
141C LYS* 3.4 3.3 - - - -
142C ILE* 2.8 44.6 + - + +
144C LEU* 3.6 30.5 - - + -
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Residues in contact with ASN 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASN 3.6 0.9 - - - +
67C TRP* 3.2 11.1 - - - -
68C THR* 2.8 47.5 + - - +
70C GLN* 2.8 31.1 + - - +
77C GLU* 3.5 3.8 + - - -
124C ILE* 4.3 3.0 + - - +
125C TYR* 1.3 76.5 - - - +
127C CYS* 1.3 58.3 + - - +
128C TYR* 3.2 28.4 + - + -
139C HIS* 2.8 23.2 + - - +
140C GLY 3.3 3.1 - - - -
141C LYS* 3.3 22.4 - - - +
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Residues in contact with CYS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C VAL* 4.1 1.3 - - - -
34C VAL* 4.3 0.9 - - - -
50C CYS* 2.6 50.9 - - - -
65C LEU* 5.4 0.9 - - + -
66C ASN 3.4 4.3 - - - +
67C TRP* 3.6 32.2 - - + +
110C VAL* 4.8 10.3 - - + -
126C ASN* 1.3 71.0 - - - +
128C TYR* 1.3 62.0 + - - +
129C ILE* 4.2 5.9 - - + +
138C GLY 3.7 0.5 - - - +
139C HIS* 3.2 7.8 - - - -
140C GLY* 2.8 47.8 + - - -
142C ILE* 5.7 0.4 - - - -
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Residues in contact with TYR 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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64C SER 4.0 0.7 - - - +
65C LEU* 3.5 3.5 - - - +
66C ASN* 2.8 52.4 + - + +
68C THR* 3.8 12.3 - - + -
77C GLU* 2.7 34.3 + - - -
126C ASN* 3.2 33.2 + - + -
127C CYS* 1.3 73.6 - - - +
129C ILE* 1.3 62.8 + - - +
130C MET 4.2 0.4 + - - -
137C ARG* 2.1 63.5 - - - +
138C GLY 3.3 4.3 - - - -
139C HIS* 3.7 30.3 + + - -
301C NAG 4.9 8.4 - - - +
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Residues in contact with ILE 129 (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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30C MET* 2.9 12.5 - - + +
32C VAL* 4.3 23.3 - - + -
52C PHE* 2.8 47.3 - - + -
63C PHE* 2.7 46.2 - - + -
64C SER 3.7 2.5 - - - +
65C LEU* 4.5 4.3 - - + -
110C VAL* 4.6 15.0 - - + -
127C CYS* 4.8 5.4 - - + +
128C TYR* 1.3 80.6 - - - +
130C MET* 1.3 60.3 - - - +
131C ASN* 5.2 0.4 - - + -
137C ARG* 3.3 3.7 - - - -
138C GLY* 2.7 40.6 + - - +
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Residues in contact with MET 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C MET* 4.1 2.0 - - - -
62C GLN 4.0 3.3 - - - +
63C PHE* 3.9 0.8 - - - -
64C SER* 3.2 35.9 + - - +
128C TYR 4.2 0.6 - - - -
129C ILE* 1.3 73.3 - - - +
131C ASN* 1.3 63.5 + - - +
132C PRO* 4.0 11.6 - - - +
134C ASP 4.8 4.9 - - - +
135C ARG* 4.6 12.6 - - - +
136C HIS 4.6 4.5 - - - +
137C ARG* 4.2 20.6 - - + -
301C NAG 4.8 22.0 + - + +
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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
------------------------------------------------------------
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