Contacts of the strand formed by residues 123 - 135 (chain C) in PDB entry 4COF
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 THR 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C TYR* 3.5 40.9 + - + +
67C TRP 3.4 20.9 - - - +
68C ARG* 4.0 10.5 - - + +
118C LEU* 3.6 3.3 - - - -
119C HIS* 2.7 48.4 + - - +
121C ASP* 2.7 30.3 + - - +
122C GLY* 1.4 74.8 - - - +
124C VAL* 1.3 56.6 + - - +
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Residues in contact with VAL 124 (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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65C GLN 3.6 1.4 - - - +
66C TYR* 3.2 28.5 - - - +
67C TRP* 2.8 58.5 + - + +
69C ASP* 4.6 0.7 - - + -
72C LEU* 3.7 30.5 - - + -
91C LEU* 4.9 3.1 - - + -
116C ILE* 4.2 18.4 - - + -
117C ARG 3.6 3.1 - - - -
118C LEU* 3.9 14.1 - - + -
119C HIS* 4.7 1.1 - - - -
122C GLY 4.0 6.7 - - - +
123C THR* 1.3 75.3 - - - +
125C LEU* 1.3 68.2 + - - +
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Residues in contact with LEU 125 (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 GLN* 3.7 32.8 - - + +
65C GLN 3.6 8.1 - - - +
66C TYR* 4.8 6.3 - - + +
115C MET* 3.3 24.0 - - + +
116C ILE* 3.5 1.6 - - - -
117C ARG* 3.0 71.0 + - + +
119C HIS* 4.0 13.9 - - + +
124C VAL* 1.3 73.7 - - - +
126C TYR* 1.4 59.9 + - - +
169C ARG* 4.3 18.4 - - - +
202D THR* 4.2 12.6 - - + -
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Residues in contact with TYR 126 (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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110B THR* 5.1 6.2 + - - -
111B VAL* 6.2 0.8 - - + +
63C PHE 3.6 1.9 - - - +
64C GLN* 3.4 2.8 - - - -
65C GLN* 2.8 64.1 + - + +
67C TRP* 3.5 26.5 - + + -
88C ALA* 4.1 5.5 - - + +
93C VAL* 3.7 35.6 - - + +
94C PRO 5.7 0.7 - - - -
112C LYS* 5.7 0.9 + - - -
114C ARG* 3.7 32.3 + - + -
115C MET* 3.3 5.4 - - - -
116C ILE* 3.5 25.4 - - + -
125C LEU* 1.4 72.1 - - - +
127C GLY* 1.3 66.2 + - - +
128C LEU* 3.6 26.9 - - + +
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Residues in contact with GLY 127 (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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63C PHE 3.5 5.8 - - - -
64C GLN* 4.5 8.5 - - - -
114C ARG* 3.2 7.8 - - - +
115C MET* 2.9 50.4 + - - +
126C TYR* 1.3 72.9 - - - +
128C LEU* 1.3 64.4 + - - +
157D TYR* 3.7 9.6 - - - -
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Residues in contact with LEU 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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110B THR* 3.9 36.8 - - + +
61C MET 3.6 1.0 - - - +
62C TYR* 3.6 0.2 - - - -
63C PHE* 2.7 44.1 + - + +
65C GLN* 4.7 3.6 - - - +
106C VAL* 4.0 27.8 - - + -
112C LYS* 5.2 3.4 - - - +
113C ASN 3.4 3.4 - - - +
114C ARG* 3.8 16.8 - - + -
126C TYR* 3.6 36.1 - - + +
127C GLY* 1.3 78.8 - - - +
129C ARG* 1.4 58.8 + - - +
130C ILE* 4.0 15.9 - - + -
157D TYR* 3.1 7.8 + - - -
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Residues in contact with ARG 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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45C ALA* 5.6 2.8 - - - +
60C THR* 4.0 19.9 - - + +
61C MET 3.3 12.8 - - - +
62C TYR* 3.7 28.7 + - + -
106C VAL* 3.3 5.0 - - - +
107C HIS* 3.1 56.5 + - + -
109C VAL 5.8 0.2 + - - -
113C ASN* 2.8 45.0 + - + -
128C LEU* 1.4 70.7 - - - +
130C ILE* 1.3 59.0 + - - +
97D TYR* 3.7 10.3 - - - -
98D PHE 3.2 22.1 + - - +
99D LEU 3.4 19.7 + - - -
101D ASP* 3.3 26.7 + - - +
157D TYR* 3.2 9.1 + - + +
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Residues in contact with ILE 130 (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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109B VAL* 3.7 29.8 - - + -
110B THR* 4.0 15.7 - - + -
59C LEU 3.8 0.7 - - - +
60C THR* 3.3 2.9 - - - -
61C MET* 2.9 43.0 + - + +
63C PHE* 3.6 27.6 - - + -
98C PHE* 4.0 8.5 - - + -
104C SER* 4.3 1.8 - - - +
105C PHE 3.3 9.9 - - - +
106C VAL* 3.8 17.0 - - + -
107C HIS* 4.3 1.6 - - - -
128C LEU* 4.0 11.9 - - + +
129C ARG* 1.3 77.2 - - - +
131C THR* 1.4 66.3 + - - +
132C THR* 3.3 22.8 + - - +
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Residues in contact with THR 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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48C ASP* 4.8 1.3 - - - +
58C THR* 3.7 25.6 - - + -
59C LEU 3.3 3.8 - - - +
60C THR* 3.0 22.1 + - - +
103C LYS 4.2 0.2 - - - +
104C SER* 3.2 4.2 - - - -
105C PHE* 3.0 60.7 + - + -
107C HIS* 2.6 27.2 + - - -
130C ILE* 1.4 69.3 - - - +
132C THR* 1.3 61.6 + - - +
133C THR* 5.5 0.2 - - - +
102D LYS 4.6 1.8 + - - +
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Residues in contact with THR 132 (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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57C TYR 3.7 1.0 - - - +
58C THR* 3.3 3.4 - - - -
59C LEU* 2.8 42.1 + - + +
61C MET* 3.7 14.3 - - - +
98C PHE* 3.9 5.7 - - + -
101C ASP* 3.7 12.3 - - + +
103C LYS 3.7 0.2 - - - -
104C SER* 2.9 23.8 + - - +
130C ILE* 3.3 17.5 - - - +
131C THR* 1.3 70.9 - - - +
133C THR* 1.3 68.6 + - - +
134C ALA* 3.8 5.2 + - + +
152C LEU* 4.0 25.1 - - + -
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Residues in contact with THR 133 (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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49C MET* 5.3 1.0 - - + +
56C ASP* 3.7 35.0 - - + +
57C TYR 3.4 4.7 - - - +
58C THR* 2.9 27.9 + - - +
101C ASP* 3.7 1.9 - - - +
102C LYS* 2.7 41.8 + - + +
103C LYS* 2.9 21.8 + - - +
131C THR* 5.5 0.3 - - - +
132C THR* 1.3 70.5 - - - +
134C ALA* 1.3 53.0 + - - +
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Residues in contact with ALA 134 (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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56C ASP* 3.1 6.4 - - - +
57C TYR* 2.9 58.7 + - + +
100C ASN* 3.4 27.8 - - - +
101C ASP* 4.4 0.4 - - - +
102C LYS* 4.4 0.4 - - - -
132C THR* 3.7 5.7 - - + -
133C THR* 1.3 74.3 - - - +
135C ALA* 1.3 60.2 + - - +
152C LEU* 4.1 14.8 - - + -
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Residues in contact with ALA 135 (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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48B ASP* 5.9 0.9 - - - +
55C MET 3.9 8.3 - - - +
56C ASP* 4.0 4.0 - - - -
57C TYR* 4.1 2.9 - - - -
100C ASN* 2.9 40.4 + - + +
102C LYS* 4.1 17.9 - - + +
134C ALA* 1.3 72.7 - - - +
136C CYS* 1.3 59.6 + - - +
137C MET 4.1 1.6 - - - +
151C THR* 4.4 1.9 + - - +
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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