Contacts of the strand formed by residues 70 - 75 (chain P) in PDB entry 3K9Q
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 70 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P GLN* 4.8 17.4 - - - +
28P GLU* 4.2 39.7 + - - +
66P ARG* 3.2 5.3 - - - -
67P VAL* 2.8 46.9 + - + +
68P ASN* 3.2 8.2 - - - +
69P GLY* 1.3 73.8 - - - +
71P GLU* 1.3 65.8 + - - +
72P VAL* 3.5 5.4 + - + +
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Residues in contact with GLU 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P VAL 4.8 2.6 - - - +
30P VAL* 4.3 7.3 - - - +
61P VAL* 4.1 18.6 - - + +
62P ASP 3.5 20.8 - - - +
63P GLY 5.1 0.2 - - - +
65P PHE 3.9 1.8 - - - -
66P ARG* 4.4 10.5 - - + +
69P GLY 4.1 1.4 + - - -
70P LYS* 1.3 75.5 - - - +
72P VAL* 1.3 67.3 + - - +
73P LYS* 4.0 32.3 + - + +
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Residues in contact with VAL 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P PHE* 3.9 23.8 - - + -
29P VAL* 3.7 19.5 - - + +
30P VAL 3.8 2.2 - - - -
31P ALA* 4.1 7.4 - - - +
32P VAL* 4.0 19.7 - - + +
64P GLY* 3.3 2.8 - - - -
65P PHE* 2.8 68.3 + - + +
67P VAL* 4.6 3.6 - - + -
70P LYS* 4.5 7.6 - - + +
71P GLU* 1.3 79.3 - - - +
73P LYS* 1.3 75.3 + - - +
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Residues in contact with LYS 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P VAL 3.0 16.9 + - - +
31P ALA* 3.0 6.0 - - + -
32P VAL 2.8 24.4 + - - -
62P ASP 5.2 1.3 - - - +
63P GLY* 3.6 15.3 - - - +
71P GLU* 4.0 29.8 - - - +
72P VAL* 1.3 76.2 - - - +
74P SER* 1.3 60.1 + - - +
75P PHE* 4.1 24.1 - - + -
88P LEU* 4.7 18.6 - - + +
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Residues in contact with SER 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P VAL* 3.2 8.7 - - - -
38P ASP* 2.4 35.8 + - - -
41P LEU* 4.0 17.8 - - - +
63P GLY* 3.1 13.9 + - - +
64P GLY* 3.6 7.5 - - - -
65P PHE* 4.2 8.3 - - - -
72P VAL 3.8 0.2 + - - -
73P LYS* 1.3 75.6 - - - +
75P PHE* 1.3 73.7 + - - +
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Residues in contact with PHE 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P ALA* 4.2 3.6 - - + -
32P VAL 3.0 15.0 + - - +
33P ASN* 3.1 20.6 - - - +
34P ASP* 3.2 16.1 + - - +
36P THR 4.9 2.8 - - - +
41P LEU* 5.3 3.5 - - - +
63P GLY 6.1 0.2 - - - -
73P LYS* 4.1 23.8 - - + -
74P SER* 1.3 80.3 - - - +
76P SER* 1.3 62.2 + - - +
77P GLU* 4.6 2.2 - - + +
83P LEU* 4.0 8.7 - - + -
84P PRO* 3.4 37.0 - - + -
85P TRP* 4.5 8.7 - + - -
88P LEU* 3.7 30.3 - - + -
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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