Contacts of the strand formed by residues 102 - 113 (chain C) in PDB entry 3O4O
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 TYR 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C VAL* 6.1 0.2 - - - +
52C ILE* 3.0 24.8 - - + +
97C THR* 4.0 27.2 - - - +
98C ARG* 3.6 6.6 + - - -
99C ASN* 2.0 81.4 + - + +
100C ALA 3.2 1.5 - - - -
101C SER* 1.3 71.8 - - - +
103C CYS* 1.3 72.2 + - - +
104C ASP* 4.2 8.7 - - - +
337C NAG 3.7 36.3 - - + -
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Residues in contact with CYS 103 (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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15C CYS* 1.9 50.2 - - - +
16C ARG* 3.3 21.7 + - - +
96C THR* 6.0 2.0 - - - -
97C THR 3.1 22.2 - - - +
98C ARG* 3.3 25.6 - - - +
102C TYR* 1.3 83.8 - - - +
104C ASP* 1.3 70.8 + - - +
105C LYS* 5.6 1.8 - - - -
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Residues in contact with ASP 104 (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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15C CYS* 4.3 0.9 - - - -
16C ARG* 3.0 39.8 + - + +
18C ARG* 3.4 28.2 - - + +
40C VAL* 5.5 4.1 - - - +
96C THR* 3.8 1.2 - - - -
97C THR* 2.6 56.0 + - - +
102C TYR* 4.2 8.7 - - - -
103C CYS* 1.3 84.5 - - - +
105C LYS* 1.3 70.6 + - - +
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Residues in contact with LYS 105 (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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15C CYS* 5.0 13.7 - - + +
16C ARG 3.1 13.7 + - - +
17C PHE* 3.7 22.3 - - + -
18C ARG 2.9 25.3 + - - -
19C GLY 3.9 0.7 + - - -
57C HIS* 4.5 11.4 + - - -
94C VAL* 3.7 26.5 - - + +
95C CYS* 3.2 17.0 - - - +
96C THR* 4.5 6.5 - - + -
103C CYS* 5.6 2.7 - - - -
104C ASP* 1.3 85.2 - - - +
106C MET* 1.3 66.5 + - - +
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Residues in contact with MET 106 (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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17C PHE* 4.6 2.9 - - - -
18C ARG* 3.6 29.4 - - + -
19C GLY* 3.4 25.8 - - - +
20C ARG 4.6 1.6 - - - +
21C HIS* 4.5 10.8 - - - +
37C CYS* 5.5 0.4 - - - -
38C PRO* 3.3 56.9 - - + +
39C GLN* 4.2 19.1 - - + +
40C VAL* 4.9 7.2 - - + -
56C TRP* 5.0 0.2 + - - -
94C VAL* 3.0 5.0 - - - -
95C CYS* 2.8 29.7 + - + +
105C LYS* 1.3 85.1 - - - +
107C SER* 1.3 59.8 + - - +
108C ILE 4.2 0.2 + - - -
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Residues in contact with SER 107 (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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17C PHE* 4.1 12.4 - - - -
19C GLY 3.5 4.6 + - - -
20C ARG* 3.6 24.6 - - - +
21C HIS* 2.8 32.6 + - - +
38C PRO* 4.0 2.0 - - - -
92C THR* 3.9 20.7 - - - +
93C TYR 2.6 18.8 - - - -
94C VAL* 4.2 9.2 - - - -
106C MET* 1.3 73.6 - - - +
108C ILE* 1.3 59.5 + - - +
109C GLU 4.1 0.9 + - - -
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Residues in contact with ILE 108 (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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21C HIS* 4.0 24.5 - - + -
23C LYS 4.3 6.3 - - - +
25C GLU* 4.4 13.2 - - - +
35C LEU* 4.0 28.3 - - + -
36C ARG 3.2 25.6 - - - +
37C CYS* 4.3 1.1 - - - -
38C PRO* 3.2 33.4 - - + -
56C TRP* 4.5 10.5 - - - +
92C THR* 3.7 2.5 - - - -
93C TYR* 3.0 35.5 + - + +
107C SER* 1.3 72.8 - - - +
109C GLU* 1.3 71.2 + - - +
110C LEU* 4.8 0.2 - - - +
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Residues in contact with GLU 109 (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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20C ARG* 5.0 10.6 + - + +
21C HIS 5.2 3.0 + - - -
24C ARG* 3.5 47.8 + - + +
25C GLU* 3.7 15.2 + - - +
26C PHE* 5.5 2.4 - - + -
35C LEU* 5.1 0.2 - - - +
91C GLY 3.8 5.6 - - - +
92C THR* 4.4 18.5 + - + +
107C SER* 4.1 2.0 + - - -
108C ILE* 1.3 84.6 - - - +
110C LEU* 1.3 82.4 + - - +
111C ARG* 4.4 15.3 - - + +
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Residues in contact with LEU 110 (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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25C GLU* 3.7 16.4 - - + +
27C ARG* 5.2 3.8 - - + -
33C VAL* 3.9 12.8 - - + -
35C LEU* 3.5 42.6 - - + -
82C LEU* 4.7 9.6 - - + -
89C ASP* 4.8 2.0 - - + +
90C SER* 3.5 5.6 - - - -
91C GLY* 2.9 35.8 + - - +
93C TYR* 4.4 16.8 - - + +
109C GLU* 1.3 85.0 - - - +
111C ARG* 1.3 89.5 + - - +
112C VAL* 3.6 28.7 - - + +
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Residues in contact with ARG 111 (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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25C GLU 3.2 5.7 + - - +
26C PHE* 3.3 30.6 - - + -
27C ARG 3.1 25.5 + - - +
90C SER* 3.9 13.8 + - - -
109C GLU* 4.4 13.7 - - - +
110C LEU* 1.3 85.5 - - - +
112C VAL* 1.3 67.2 + - - +
113C PHE* 3.6 39.7 + - + -
119C PHE* 5.6 1.8 - - - -
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Residues in contact with VAL 112 (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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27C ARG* 3.4 8.7 - - + +
28C LEU 3.9 2.0 - - - +
29C GLU* 3.5 22.4 - - - +
33C VAL* 5.2 0.2 - - + -
82C LEU* 6.1 0.2 - - + -
85C ALA* 4.2 19.5 - - + +
86C LEU 3.8 14.8 - - - +
87C GLN* 3.6 33.2 + - - +
89C ASP* 4.5 5.8 - - + -
90C SER* 3.3 19.0 + - - +
110C LEU* 3.6 21.5 - - + -
111C ARG* 1.3 79.7 + - - +
113C PHE* 1.3 76.5 + - - +
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Residues in contact with PHE 113 (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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34A GLN* 4.7 3.4 - - - -
26C PHE* 3.5 36.8 - + + -
27C ARG 3.1 14.4 + - - -
28C LEU* 4.0 9.2 - - + -
29C GLU* 2.7 37.7 + - - +
87C GLN* 4.6 4.5 - - - +
111C ARG* 3.6 46.4 - - + -
112C VAL* 1.3 76.0 - - - +
114C GLU* 1.3 61.6 + - - +
119C PHE* 3.1 40.2 - + + -
122C PHE* 4.2 21.3 - + + -
123C ILE* 3.5 21.3 - - + -
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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