Contacts of the strand formed by residues 17 - 23 (chain C) in PDB entry 4YC3
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 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C PHE* 3.4 3.1 - - - -
14C ASP* 2.9 32.0 + - - -
16C HIS* 1.3 94.4 - + + +
18C GLU* 1.3 61.9 + - - +
19C TYR* 3.5 36.7 - - + -
70C ARG* 3.5 56.4 + - + -
71C ARG 3.5 2.7 - - - +
72C PRO* 3.7 33.4 - - + -
73C LEU* 3.3 12.2 - - - +
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Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LYS* 4.0 20.1 + - + +
12C TYR 3.4 8.5 - - - +
13C PHE* 4.2 6.5 - - + -
17C TYR* 1.3 75.9 - - - +
19C TYR* 1.3 62.1 + - - +
54C TRP* 3.5 21.3 - - + -
70C ARG* 3.3 4.0 - - - +
71C ARG* 2.9 76.1 + - + +
72C PRO 4.2 5.3 - - - +
73C LEU* 3.7 14.0 - - + +
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Residues in contact with TYR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A THR 4.5 3.2 + - - -
241A PHE 4.5 2.1 + - - -
242A PRO* 3.5 36.0 - - + +
11C LYS* 3.3 10.4 - - - +
12C TYR* 2.8 61.4 + + + +
13C PHE* 4.2 4.0 - - - -
14C ASP* 3.0 32.8 + - - -
17C TYR* 3.5 26.0 - - + -
18C GLU* 1.3 75.4 - - - +
20C ARG* 1.3 64.6 + - - +
54C TRP* 3.9 3.1 - - - -
57C TYR* 3.5 28.3 - + - +
69C PHE 3.3 2.9 - - - +
70C ARG* 3.4 34.4 + - + -
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Residues in contact with ARG 20 (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 TYR* 3.6 32.6 - - - +
9C SER* 3.2 32.7 + - - +
10C ASP 4.3 0.9 - - - +
11C LYS* 4.4 17.7 - - + +
12C TYR* 3.8 8.8 + - - -
19C TYR* 1.3 77.6 - - - +
21C HIS* 1.3 70.9 + - - +
22C VAL* 4.8 4.3 - - + -
49C GLN 5.2 0.2 + - - -
50C GLN* 3.0 43.0 + - - +
51C SER* 4.8 1.4 + - - +
54C TRP* 3.8 31.1 - - + +
57C TYR* 5.0 0.2 - - - -
68C LEU* 3.7 0.9 - - - +
69C PHE* 2.8 37.5 + - + +
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Residues in contact with HIS 21 (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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207A ASP* 3.3 29.1 + - - -
208A SER* 4.1 2.6 + - - -
210A ILE* 4.7 2.1 - - + +
211A ASP* 3.3 28.5 + - + +
214A PHE* 5.5 1.8 - + - -
7C TYR 4.1 0.2 - - - +
9C SER* 2.8 58.3 + - - -
12C TYR* 3.1 27.8 - + - -
20C ARG* 1.3 75.7 - - - +
22C VAL* 1.3 66.4 + - - +
23C MET* 4.0 10.2 - - + +
66C ILE* 3.9 18.4 - - + +
67C LEU 3.1 12.1 - - - +
68C LEU* 4.0 18.6 - - + -
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Residues in contact with VAL 22 (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 ILE* 3.2 35.9 - - + -
7C TYR 3.2 6.1 - - - +
8C TYR* 3.7 18.6 - - + -
20C ARG* 4.8 7.4 - - + -
21C HIS* 1.3 80.4 - - - +
23C MET* 1.3 60.7 + - - +
24C LEU* 4.3 4.0 - - + -
48C VAL* 4.2 15.5 - - + -
50C GLN* 4.8 4.3 - - - +
65C HIS 3.4 1.9 - - - +
66C ILE* 3.4 4.0 - - - -
67C LEU* 2.8 41.5 + - + +
69C PHE* 3.6 30.5 - - + -
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Residues in contact with MET 23 (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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207A ASP* 3.8 36.8 - - + +
208A SER* 4.7 0.7 - - - -
5C GLN 4.4 1.0 - - - +
6C ILE* 3.7 6.4 - - - +
7C TYR* 2.9 68.7 + - + +
9C SER* 5.4 0.2 - - - -
21C HIS* 4.0 19.7 - - + +
22C VAL* 1.3 72.3 - - - +
24C LEU* 1.3 64.0 + - - +
25C PRO* 4.3 0.3 - - - +
65C HIS* 3.5 12.6 - - + -
66C ILE* 4.0 26.5 - - + -
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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