Contacts of the strand formed by residues 6 - 11 (chain K) in PDB entry 3MGO
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 6 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232J GLU* 4.4 18.8 - - + +
4K THR* 3.6 4.5 + - + +
5K PRO* 1.3 73.2 - - - +
7K ILE* 1.3 60.3 + - - +
8K GLN* 5.7 2.2 - - + -
26K TYR 3.4 1.5 - - - +
27K VAL* 3.2 8.1 - - - -
28K SER* 2.7 46.4 + - - +
29K GLY* 5.3 4.9 - - - -
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Residues in contact with ILE 7 (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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5K PRO* 3.8 13.0 - - + +
6K LYS* 1.3 81.1 - - - +
8K GLN* 1.3 73.7 + - - +
9K VAL* 4.4 2.9 - - + -
25K CYS* 4.0 24.0 - - - -
26K TYR 3.5 2.5 - - - +
27K VAL* 4.5 3.4 - - + -
80K CYS* 4.4 1.6 - - + -
82K VAL* 3.6 37.7 - - + -
87K LEU* 5.4 0.2 - - + -
91K LYS* 4.0 33.2 - - + +
93K VAL* 3.9 31.5 - - + +
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Residues in contact with GLN 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231J VAL* 3.6 19.4 - - - +
232J GLU* 3.0 44.9 + - - +
234J ARG* 3.0 39.7 + - - +
6K LYS* 5.7 2.2 - - + -
7K ILE* 1.3 81.4 - - - +
9K VAL* 1.3 63.3 + - - +
10K TYR* 3.5 17.7 - - + -
25K CYS* 3.3 3.5 - - - -
26K TYR* 2.8 48.2 + - + +
93K VAL* 5.8 0.4 - - - -
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Residues in contact with VAL 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234J ARG* 4.7 0.5 + - - -
7K ILE* 4.4 1.8 - - + -
8K GLN* 1.3 75.8 - - - +
10K TYR* 1.3 69.2 + - - +
23K LEU* 4.1 13.0 - - + -
24K ASN 3.3 9.9 - - - +
25K CYS* 4.9 0.7 - - + -
39K LEU* 6.1 0.7 - - + -
79K ALA 4.6 3.1 - - - -
80K CYS* 3.4 38.4 - - + +
93K VAL* 3.5 33.5 - - + +
94K LYS 4.5 1.3 - - - +
95K TRP* 3.8 35.3 - - + -
96K ASP 4.9 1.2 + - - -
99K MET* 4.3 10.7 - - - +
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Residues in contact with TYR 10 (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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234J ARG* 3.4 54.7 - - - +
235J PRO* 2.7 33.5 + - - +
242J GLN* 3.3 21.5 - - - -
8K GLN* 3.5 22.2 - - + -
9K VAL* 1.3 81.6 - - - +
11K SER* 1.3 63.1 - - - +
23K LEU* 3.7 2.4 - - - +
24K ASN* 2.6 64.5 + - + +
26K TYR* 3.4 25.7 - - + +
65K LEU* 3.6 5.4 - - - +
95K TRP* 3.8 13.7 - - - +
99K MET* 4.0 5.4 - - - +
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Residues in contact with SER 11 (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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234J ARG* 5.2 0.7 + - - -
242J GLN* 3.5 12.0 + - - +
10K TYR* 1.3 82.8 - - - +
12K ARG* 1.3 66.5 + - - +
13K HIS 2.6 25.2 + - - +
14K PRO* 4.5 0.7 - - - +
15K ALA* 3.9 8.4 + - - +
21K ASN* 3.8 11.7 - - - -
22K PHE 3.1 11.2 - - - -
23K LEU* 4.7 0.2 - - - +
70K PHE* 4.2 6.3 - - - -
95K TRP* 3.8 24.6 + - - +
97K ARG 5.7 0.9 + - - -
99K MET* 5.3 0.4 + - - -
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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