Contacts of the strand formed by residues 18 - 23 (chain L) in PDB entry 4YHP
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 ALA 18 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L VAL* 4.2 13.2 - - + -
11L SER 5.8 0.2 - - - -
12L VAL* 4.0 18.7 - - + +
16L GLN 4.0 0.2 + - - -
17L THR* 1.3 74.2 - - - +
19L ARG* 1.3 63.9 + - - +
20L ILE* 4.3 2.0 - - + -
72L LEU 3.7 0.6 - - - +
73L THR* 3.4 4.3 - - - -
74L ILE* 2.6 53.0 + - + +
77L VAL* 3.9 16.4 - - + -
105L VAL* 4.8 6.5 - - + -
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Residues in contact with ARG 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F ALA 5.8 2.4 + - - -
162F GLU* 5.3 8.5 + - - -
7L PRO* 5.5 0.5 - - - +
10L VAL* 3.5 21.4 - - - +
17L THR* 4.0 29.4 + - + +
18L ALA* 1.3 79.1 - - - +
20L ILE* 1.3 63.2 + - - +
21L THR* 4.1 2.1 + - - -
71L THR* 4.3 13.0 - - + -
72L LEU 3.5 2.7 - - - -
73L THR* 3.8 21.7 + - - +
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Residues in contact with ILE 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L GLN* 3.8 3.8 - - - +
10L VAL* 4.3 7.6 - - + -
18L ALA* 5.2 1.1 - - + -
19L ARG* 1.3 79.2 - - - +
21L THR* 1.3 63.2 + - - +
34L TRP* 3.5 21.5 - - + -
71L THR* 3.3 6.2 - - - +
72L LEU* 2.8 57.3 + - + +
74L ILE* 4.1 10.1 - - + -
85L TYR* 3.8 24.0 - - + -
103L THR* 3.4 38.8 - - + +
105L VAL* 3.8 27.4 - - + -
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Residues in contact with THR 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F SER* 5.0 16.2 - - - -
5L THR* 4.1 9.6 - - - +
6L GLN* 3.5 12.5 - - - +
7L PRO* 3.2 32.5 - - + +
19L ARG 4.1 2.0 + - - -
20L ILE* 1.3 76.1 - - - +
22L CYS* 1.3 68.6 + - - +
23L GLY* 4.2 3.4 - - - +
34L TRP* 4.0 1.9 - - - -
69L THR* 3.7 21.3 - - + +
70L ALA 3.6 2.9 - - - -
71L THR* 4.4 5.9 + - - +
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Residues in contact with CYS 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LEU* 3.8 26.5 - - - -
5L THR 3.7 2.0 - - - -
6L GLN* 4.6 0.2 - - - -
21L THR* 1.3 73.2 - - - +
23L GLY* 1.3 59.3 + - - +
27L ILE* 3.7 9.4 - - - +
32L VAL* 4.6 2.2 - - - -
34L TRP* 3.4 21.3 - - + -
69L THR* 3.4 2.7 - - - -
70L ALA* 2.8 43.5 + - + +
87L CYS* 2.0 48.9 - - + -
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Residues in contact with GLY 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L VAL 3.3 8.7 - - - +
4L LEU* 3.4 1.9 - - - -
5L THR* 3.0 47.7 + - - +
21L THR* 4.1 4.6 - - - +
22L CYS* 1.3 74.4 - - - +
24L GLY* 1.3 58.3 + - - -
27L ILE* 4.5 3.1 - - - -
68L ASN 3.6 9.9 - - - -
69L THR* 4.6 2.9 - - - -
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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