Contacts of the strand formed by residues 3 - 14 (chain C) in PDB entry 3BZE
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 HIS 3 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C SER* 1.3 81.7 + - - +
4C SER* 1.4 61.0 + - - +
29C ASP* 3.2 24.5 + - - +
102C GLU* 3.2 2.9 - - - +
103C LEU* 2.5 38.8 + - + +
107C ARG* 2.7 57.0 + - - -
168C LEU* 3.5 8.9 - - + +
172C LEU* 3.7 34.3 - - + +
179C LEU 5.4 2.7 - - - -
180C LEU* 3.4 26.0 - - + +
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Residues in contact with SER 4 (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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3C HIS* 1.4 76.7 - - - +
5C LEU* 1.3 62.6 + - - +
6C LYS* 4.0 20.1 - - - -
27C TYR 4.0 0.7 - - - -
28C VAL* 3.4 7.4 - - - +
29C ASP* 2.6 48.6 + - - -
101C CYS 3.3 5.8 - - - -
102C GLU* 3.8 23.1 - - - -
168C LEU* 3.5 7.1 - - - +
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Residues in contact with LEU 5 (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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4C SER* 1.3 76.2 - - - +
6C LYS* 1.3 60.1 + - - +
7C TYR* 4.2 13.6 - - + +
27C TYR 3.3 7.4 - - - +
28C VAL* 5.2 1.6 - - + -
33C PHE* 4.0 19.1 - - + -
100C GLY* 3.7 0.7 - - - -
101C CYS* 3.1 28.1 + - - +
159C TYR* 4.6 6.9 + - - +
164C CYS* 3.2 49.8 - - - +
167C TRP* 4.4 4.9 - - + -
168C LEU* 3.7 24.5 - - + +
171C TYR* 3.5 29.2 - - + -
1Q VAL 4.6 2.5 - - - +
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Residues in contact with LYS 6 (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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4C SER* 4.0 24.7 - - - +
5C LEU* 1.3 75.5 - - - +
7C TYR* 1.3 61.8 + - - +
8C PHE* 3.1 41.9 - - + -
25C VAL 4.4 0.2 - - - +
27C TYR* 3.3 50.0 + - - +
29C ASP 4.4 5.8 + - - -
99C HIS* 2.6 22.4 - - - +
100C GLY* 3.4 5.8 - - - -
101C CYS 4.8 0.2 - - - +
102C GLU* 6.1 0.7 - - + +
113C TYR* 2.3 32.3 - - + +
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Residues in contact with TYR 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 4.2 10.0 - - + +
6C LYS* 1.3 74.4 - - - +
8C PHE* 1.3 76.6 + - - +
9C HIS* 3.7 13.7 - + + +
24C SER* 5.7 2.5 - - - -
25C VAL 3.3 7.0 - - - +
26C GLY* 3.0 37.5 - - - -
33C PHE* 3.2 25.8 - + - -
34C VAL* 3.7 13.9 - - + +
45C MET* 5.4 3.8 - - + -
59C TYR* 4.6 1.6 + - - -
63C GLU* 4.4 3.7 + - - -
97C TRP 4.5 0.4 - - - -
98C MET* 3.3 18.1 - - - +
99C HIS* 3.1 39.6 + + + +
159C TYR* 3.8 2.5 - - - -
171C TYR* 4.0 1.6 + - - -
1Q VAL* 3.4 22.5 + - - -
2Q MET* 3.3 33.8 + - + -
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Residues in contact with PHE 8 (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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6C LYS* 3.1 53.2 - - + -
7C TYR* 1.3 91.9 - - - +
9C HIS* 1.3 63.4 + - - +
10C THR* 3.9 1.7 + - - -
23C ILE 3.8 4.7 - - - +
24C SER* 3.8 0.2 - - - -
25C VAL* 3.1 32.9 + - + +
27C TYR* 4.0 20.2 - + - -
97C TRP 3.7 2.7 - - - -
98C MET* 3.5 28.9 - - + -
113C TYR* 4.7 1.3 - + - -
54D LEU 5.1 2.8 - - - +
55D SER* 3.5 20.0 - - - +
56D PHE* 3.5 42.6 - + + +
57D SER* 5.5 3.6 - - - -
58D LYS 6.0 0.4 - - - -
63D TYR* 5.2 2.2 - - - -
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Residues in contact with HIS 9 (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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7C TYR* 3.7 21.4 - + + +
8C PHE* 1.3 69.1 - - - +
10C THR* 1.3 63.4 + - - +
22C PHE* 4.3 10.6 - + + -
23C ILE 3.6 4.0 - - - -
24C SER* 3.4 20.5 + - - -
74C PHE* 4.3 7.6 - - + -
95C LEU 4.5 0.9 - - - -
96C GLN* 3.2 5.7 - - - -
97C TRP* 2.7 89.2 + + + +
99C HIS* 3.0 27.7 + + - -
56D PHE* 3.6 2.6 - - - -
2Q MET* 3.7 30.7 - - + -
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Residues in contact with THR 10 (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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8C PHE 3.9 1.9 + - - -
9C HIS* 1.3 76.3 + - - +
11C SER* 1.3 63.5 + - - +
12C VAL* 4.1 13.0 - - + -
21C ARG* 3.4 1.0 - - - +
22C PHE* 3.3 6.3 - - - -
23C ILE* 2.8 47.0 + - + +
94C THR* 4.0 13.2 - - + -
95C LEU 3.7 2.7 - - - -
96C GLN* 3.8 1.6 - - + +
54D LEU* 4.4 16.4 + - + +
56D PHE* 3.3 18.7 - - - -
62D PHE* 3.4 34.6 - - + -
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Residues in contact with SER 11 (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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10C THR* 1.3 76.3 - - - +
12C VAL* 1.3 62.0 + - - +
13C SER 4.2 0.2 - - - -
20C PRO* 3.9 9.9 - - - +
21C ARG 2.9 9.9 + - - -
22C PHE* 3.9 10.1 - - - +
71C ALA 5.2 1.0 + - - -
74C PHE* 3.9 32.7 - - - +
78C LEU* 3.4 20.8 - - - +
93C HIS 3.7 1.0 - - - +
94C THR* 3.5 4.0 - - - +
95C LEU* 3.0 35.1 + - - +
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Residues in contact with VAL 12 (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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10C THR* 4.1 12.6 - - + -
11C SER* 1.3 77.6 - - - +
13C SER* 1.3 65.7 + - - +
14C ARG* 3.3 5.7 - - + +
20C PRO* 3.0 4.2 - - - +
21C ARG* 2.5 50.5 + - + +
92C SER* 3.4 20.2 - - - +
93C HIS 3.4 7.0 - - - +
94C THR* 4.1 13.7 - - - +
32D PRO* 6.1 0.7 - - + -
33D SER* 3.9 20.6 - - - +
34D ASP* 3.9 20.9 - - - +
54D LEU* 5.6 1.6 - - + -
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Residues in contact with SER 13 (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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12C VAL* 1.3 73.3 - - - +
14C ARG* 1.3 62.5 + - - +
15C PRO* 3.5 4.4 - - - +
20C PRO* 3.4 11.1 - - - +
78C LEU* 4.0 19.7 - - - +
82C ARG* 6.4 0.2 - - - -
91C GLY 4.0 4.5 + - - -
92C SER* 2.7 34.5 + - - -
93C HIS* 2.8 40.1 + - - +
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Residues in contact with ARG 14 (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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12C VAL* 3.3 13.5 - - + +
13C SER* 1.3 73.4 - - - +
15C PRO* 1.3 74.2 - - - +
16C GLY 2.9 3.2 + - - -
17C ARG* 3.0 38.4 + - + +
18C GLY 2.9 25.6 + - - +
19C GLU* 2.9 31.4 + - - +
20C PRO* 4.0 2.8 + - - +
21C ARG* 3.2 32.7 - - + +
38C ASN* 4.4 1.0 + - - +
39C ASP* 1.7 52.2 + - - -
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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