Contacts of the strand formed by residues 2 - 7 (chain C) in PDB entry 3BID
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 2 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 1.3 82.5 - - - +
3C PHE* 1.3 73.4 + - - +
4C GLU* 3.9 19.8 + - + -
17C LEU* 3.7 7.1 - - - +
18C LYS* 3.0 77.4 + - + +
19C ALA 4.2 8.5 - - - -
20C ALA* 5.9 0.4 - - - -
22C HIS* 4.9 15.2 - + - +
51D THR* 3.9 4.7 - - - -
52D PRO* 3.6 26.5 - - + +
54D LYS* 4.0 30.3 - - + +
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Residues in contact with PHE 3 (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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2C TYR* 1.3 83.6 - - - +
4C GLU* 1.3 60.6 + - - +
15C TRP* 4.1 29.6 - + + -
16C ARG 3.8 1.8 - - - -
17C LEU* 3.7 26.9 - - + -
41C VAL* 3.5 42.6 - - + -
44C LEU* 4.7 15.5 - - + -
45C LYS* 4.2 9.6 - - + -
44D LEU* 4.8 4.9 - - + -
47D THR* 4.0 21.5 - - + -
51D THR* 3.7 25.4 - - + -
52D PRO 2.9 15.1 + - - +
53D VAL* 4.3 13.0 - - + -
54D LYS 3.2 23.0 + - - -
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Residues in contact with GLU 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C TYR* 3.9 18.3 + - + -
3C PHE* 1.3 75.7 - - - +
5C ILE* 1.3 66.7 - - - +
6C TYR* 4.0 7.9 - - + -
14C ARG 3.7 0.5 - - - +
15C TRP* 3.1 5.2 - - - +
16C ARG* 3.1 55.1 + - + +
18C LYS* 3.0 42.3 + - + -
54D LYS* 3.4 11.8 - - + +
55D GLU* 5.3 0.2 - - - -
56D VAL* 4.5 22.5 - - + +
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Residues in contact with ILE 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 GLU* 1.3 74.6 - - - +
6C TYR* 1.3 69.4 + - - +
13C TYR* 4.8 6.1 - - + -
14C ARG 3.2 12.1 - - - +
15C TRP* 4.3 7.0 - - + -
34C LYS* 4.5 20.9 - - + +
37C CYS* 4.1 16.4 - - + -
38C GLN* 4.1 36.6 - - + +
41C VAL* 4.6 5.4 - - + -
53D VAL* 3.8 28.3 - - + -
54D LYS 3.3 8.2 + - - +
55D GLU* 3.3 35.6 - - + +
56D VAL* 4.1 3.1 + - - +
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Residues in contact with TYR 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLU* 4.0 12.8 - - + -
5C ILE* 1.3 77.2 - - - +
7C LYS* 1.3 72.1 + - - +
8C ASP* 4.3 5.2 - - - -
13C TYR* 3.4 11.1 - - - -
14C ARG* 2.9 81.9 + - + +
15C TRP 4.4 2.2 - - - -
16C ARG* 3.3 51.5 + - + -
27C GLN* 3.4 9.5 + - - -
56D VAL* 4.3 20.2 - - + -
9E ALA* 4.1 21.4 + - - +
10E LYS* 5.3 4.3 - - + -
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Residues in contact with LYS 7 (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 TYR* 1.3 83.6 - - - +
8C ASP* 1.3 69.9 + - - +
11C GLY* 3.2 33.6 + - - +
12C GLU 3.6 4.5 - - - +
13C TYR* 3.3 41.7 + - + -
10E LYS* 4.3 5.2 - - - +
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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