Contacts of the strand formed by residues 31 - 39 (chain K) 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 LYS 31 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C ASN 3.9 8.7 + - - -
29C GLY* 3.8 23.2 - - - -
28D ASN* 3.5 22.3 - - + +
29D GLY 2.9 24.2 + - - +
30D ILE* 3.3 45.4 - - - +
31D LYS* 3.9 4.5 + - - +
23K SER* 3.0 41.0 + - - -
24K ILE 3.5 6.3 - - - +
25K TYR* 4.0 18.8 - - + -
30K ILE* 1.3 72.6 - - - +
32K LEU* 1.3 65.4 + - - +
33K GLN* 3.9 1.2 + - - -
63K VAL* 6.1 0.4 - - - +
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Residues in contact with LEU 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LYS* 5.8 8.3 - - + -
61J THR* 4.3 8.5 - - + +
23K SER* 3.3 5.9 - - - -
24K ILE* 2.7 39.9 + - + +
26K LEU* 3.7 28.3 - - + -
30K ILE* 3.6 22.9 - - + -
31K LYS* 1.3 74.0 - - - +
33K GLN* 1.3 62.8 - - - +
46K LEU* 3.8 13.0 - - + -
52K GLN* 4.0 24.0 - - - +
54K VAL* 3.6 31.4 - - + -
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Residues in contact with GLN 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C TYR* 5.0 14.6 - - - -
29C GLY 4.2 12.6 - - - +
30D ILE* 3.2 46.8 - - + +
22K VAL 3.4 6.9 - - - +
23K SER* 3.2 22.8 + - - +
31K LYS* 3.9 2.3 + - - +
32K LEU* 1.3 81.1 - - - +
34K GLY* 1.3 59.3 + - - +
46K LEU* 3.5 13.6 - - - +
48K ASN* 3.8 22.2 + - - +
52K GLN* 4.6 2.9 + - - +
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Residues in contact with GLY 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K PRO* 3.6 4.1 - - - +
22K VAL* 2.8 34.0 + - - +
33K GLN* 1.3 76.9 - - - +
35K GLN* 1.3 64.0 + - - -
46K LEU* 3.6 7.3 - - - +
47K LYS 3.2 13.9 - - - -
48K ASN* 4.7 4.7 - - - -
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Residues in contact with GLN 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K ARG* 3.3 59.9 - - - +
20K VAL 4.0 12.3 - - - +
21K PRO* 4.5 8.4 - - + +
34K GLY* 1.3 78.5 - - - +
36K ILE* 1.3 63.1 + - - +
37K GLU 3.2 1.9 + - - -
46K LEU* 3.4 5.9 - - - +
47K LYS* 2.8 41.2 + - + +
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Residues in contact with ILE 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LEU* 3.9 25.1 - - + +
15K LEU* 3.8 34.2 + - + -
16K ARG* 2.9 46.3 - - + +
19K ARG* 6.1 0.3 - - - -
20K VAL 4.5 4.0 + - - -
22K VAL* 4.0 21.5 - - + -
24K ILE* 5.0 2.2 - - + -
35K GLN* 1.3 73.3 - - - +
37K GLU* 1.3 58.6 + - - +
38K SER 3.7 22.2 - - - +
39K PHE* 4.4 11.0 - - + -
44K ILE* 4.0 19.5 - - + -
45K LEU 3.7 3.1 - - - -
46K LEU* 4.4 4.0 - - + -
62K VAL* 4.6 4.3 - - + -
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Residues in contact with GLU 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ARG* 3.5 16.4 - - - +
35K GLN* 3.2 3.0 + - - -
36K ILE* 1.3 72.6 - - - +
38K SER* 1.3 62.4 + - - +
45K LEU* 2.8 32.1 + - + +
47K LYS* 4.1 25.6 + - + +
51K SER* 2.8 36.8 + - - -
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Residues in contact with SER 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J LEU* 3.0 30.5 - - - +
16K ARG* 4.4 9.0 - - - +
36K ILE* 3.5 2.8 - - - +
37K GLU* 1.3 84.3 - - - +
39K PHE* 1.3 75.2 + - - +
44K ILE* 3.7 4.2 - - - +
45K LEU* 2.9 35.4 + - - +
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Residues in contact with PHE 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J LEU* 3.1 17.5 - - - +
9K ASP* 3.7 30.5 - - - -
12K LEU* 3.4 41.5 - - + -
13K ASN* 3.5 34.8 - - - -
16K ARG* 4.4 10.5 - - - -
36K ILE* 4.4 9.0 - - + -
38K SER* 1.3 84.3 + - - +
40K ASP* 1.3 71.2 + - - +
43K VAL 3.4 12.3 - - - +
44K ILE* 3.9 16.2 - - + -
56K LYS* 4.2 1.6 - - - -
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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