Contacts of the strand formed by residues 107 - 111 (chain K) in PDB entry 3QUM
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 THR 107 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6K GLN* 2.9 24.2 + - - +
7K SER* 3.1 22.7 + - - +
8K GLY 3.1 28.5 - - - +
10K GLU* 4.3 0.2 - - - +
20K ILE* 3.6 37.3 - - + +
89K VAL* 3.9 1.9 - - - +
90K TYR* 3.2 32.3 + - - +
106K GLY* 1.3 71.2 - - - -
108K SER* 1.3 67.6 + - - +
109K VAL* 4.2 0.5 - - - +
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Residues in contact with SER 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K PRO* 3.4 19.9 - - - +
10K GLU 3.3 19.2 + - - -
88K ALA* 3.9 6.9 + - - -
89K VAL* 3.9 22.7 - - - +
106K GLY 4.2 1.2 + - - -
107K THR* 1.3 73.3 - - - +
109K VAL* 1.3 79.6 + - - +
110K THR* 5.1 2.6 + - - -
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Residues in contact with VAL 109 (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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10K GLU* 3.6 15.0 - - + +
12K VAL* 5.7 0.4 - - + -
18K VAL* 4.3 24.2 - - + -
20K ILE* 4.4 20.2 - - + -
82K LEU* 5.3 7.9 - - + -
86K ASP 4.7 7.4 - - - +
87K SER* 3.4 4.9 - - - -
88K ALA 3.3 30.3 + - - +
90K TYR* 4.3 17.5 - - + -
107K THR 4.2 7.6 - - - +
108K SER* 1.3 92.4 + - - +
110K THR* 1.3 69.9 + - - +
111K VAL* 4.6 9.6 - - + -
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Residues in contact with THR 110 (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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10K GLU 2.9 10.4 + - - +
11K LEU* 3.9 24.9 - - + -
12K VAL* 2.9 27.5 + - - +
87K SER* 4.0 7.0 - - - +
108K SER* 5.1 2.6 + - - -
109K VAL* 1.3 74.5 + - - +
111K VAL* 1.3 75.7 + - - +
112K SER* 4.0 6.7 - - - +
146K PHE* 4.7 6.1 - - + -
147K PRO* 5.8 2.4 - - + +
148K GLU* 6.0 2.1 - - - +
175K TYR* 5.7 6.1 - - + +
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Residues in contact with VAL 111 (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 VAL* 2.8 16.2 - - + +
13K LYS 4.0 0.4 - - - -
14K PRO* 3.7 32.9 - - + +
82K LEU* 4.1 29.4 - - + -
83K THR* 3.8 32.3 - - - +
84K SER* 4.1 11.7 - - - +
86K ASP* 5.0 2.5 - - + -
87K SER* 3.1 16.9 + - - +
109K VAL* 4.6 7.6 - - + -
110K THR* 1.3 82.8 - - - +
112K SER* 1.3 61.3 + - - +
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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