Contacts of the strand formed by residues 59 - 64 (chain L) in PDB entry 2YHT
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 ILE 59 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G TYR* 3.5 25.9 - - + +
57G HIS* 2.8 27.0 + - - -
24L ILE* 3.7 24.0 - - + -
25L TYR 3.6 12.1 - - - +
26L LEU* 4.3 0.9 - - + -
27L VAL* 4.1 1.3 - - - -
44L ILE* 3.7 31.6 - - + -
54L VAL* 3.5 22.9 - - + -
55L TYR 3.4 10.8 - - - +
56L LYS* 3.0 18.4 + - - +
58L ALA* 1.3 78.5 - - - +
60L SER* 1.3 63.5 + - - +
61L THR 3.7 7.0 - - - +
62L VAL* 3.9 9.6 - - + -
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Residues in contact with SER 60 (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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26G LEU* 3.9 18.6 - - - +
28G ASN* 3.8 10.7 + - - -
54G VAL* 3.6 4.7 - - - +
55G TYR* 2.8 30.8 + - - +
58G ALA* 3.2 24.9 - - - -
25L TYR* 2.7 20.0 + - - +
26L LEU 3.1 21.8 + - - -
27L VAL* 4.5 2.5 - - - -
58L ALA 3.7 2.2 + - - -
59L ILE* 1.3 74.6 - - - +
61L THR* 1.3 65.7 + - - -
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Residues in contact with THR 61 (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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26G LEU* 4.5 5.4 - - + -
30G ILE* 6.4 0.4 - - + -
32G LEU* 4.2 20.0 - - + -
52G GLN* 3.3 23.3 + - - +
53G MET 3.3 12.6 + - - -
54G VAL* 3.7 9.5 - - - +
23L SER 3.7 1.6 - - - +
24L ILE* 3.7 1.0 - - - -
25L TYR* 2.7 64.6 + - + +
59L ILE* 3.7 1.9 - - - +
60L SER* 1.3 88.2 + - - +
62L VAL* 1.3 62.8 + - - +
63L VAL* 4.1 4.0 - - + -
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Residues in contact with VAL 62 (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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52G GLN* 3.5 1.7 - - - -
53G MET* 2.9 50.8 + - + +
55G TYR* 4.3 3.6 - - + -
11L PHE* 3.7 20.4 - - + -
12L LEU* 4.8 2.0 - - + -
15L LEU* 4.0 14.8 - - + -
22L VAL* 4.6 13.2 - - + -
23L SER 3.7 3.4 - - - +
24L ILE* 4.5 13.5 - - + +
36L ILE* 4.6 7.9 - - + -
44L ILE* 4.8 6.5 - - + -
59L ILE* 3.9 22.7 - - + -
61L THR* 1.3 74.9 + - - +
63L VAL* 1.3 62.3 + - - +
64L PRO* 3.5 6.4 - - - +
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Residues in contact with VAL 63 (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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50G VAL* 4.3 12.3 - - + -
52G GLN* 3.4 31.9 - - + +
22L VAL* 4.5 1.8 - - - -
23L SER* 2.8 39.1 + - - +
25L TYR* 3.5 36.1 - - + -
61L THR* 4.1 1.8 - - + -
62L VAL* 1.3 76.7 - - - +
64L PRO* 1.3 77.2 - - - +
65L SER* 4.5 0.7 - - - -
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Residues in contact with PRO 64 (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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50G VAL* 3.5 26.4 - - + +
51G SER 3.3 26.7 - - - +
11L PHE* 3.7 13.7 - - + -
15L LEU* 3.5 24.5 - - + -
20L VAL* 4.4 1.8 - - + -
21L PRO 4.0 4.7 - - - +
22L VAL* 4.0 7.6 - - + -
62L VAL 3.5 8.5 - - - +
63L VAL* 1.3 91.0 - - - +
65L SER* 1.3 61.1 + - - +
66L ARG 3.2 18.2 + - - +
67L PRO* 5.8 0.2 - - + -
68L VAL* 4.5 4.3 - - + +
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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