Contacts of the strand formed by residues 37 - 41 (chain K) in PDB entry 5T0G
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 ALA 37 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36K THR* 1.3 77.0 + - - +
38K ILE* 1.3 63.7 + - - +
39K GLY 4.1 0.7 - - - -
48K LEU* 4.4 6.1 - - + -
49K ALA 3.3 14.6 - - - +
50K VAL* 3.6 15.5 - - + -
66K LYS* 5.3 0.4 - - + -
77K ALA* 5.1 2.7 - - + -
78K MET 4.8 4.7 - - - +
142K LEU* 4.0 10.7 - - + +
168K ARG 3.8 1.6 - - - +
169K ALA* 3.2 2.9 - - - -
170K ILE* 2.9 48.6 + - + +
202K LEU* 5.7 0.9 - - - -
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Residues in contact with ILE 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K THR* 4.3 8.7 - - - +
37K ALA* 1.3 77.5 - - - +
39K GLY* 1.3 64.4 + - - +
40K ILE* 4.8 10.6 - - + +
47K CYS 4.5 0.3 - - - +
48K LEU* 3.9 1.9 - - - -
49K ALA* 3.0 30.4 + - + +
168K ARG 3.5 5.2 - - - +
169K ALA* 3.7 12.3 - - + -
177K ALA* 3.7 23.3 - - + -
181K LEU* 3.9 27.6 - - + -
198K SER* 4.9 13.9 - - - +
201K ILE* 3.9 25.8 - - + -
202K LEU* 4.5 21.5 - - + +
205K VAL* 5.6 2.7 - - + -
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Residues in contact with GLY 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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37K ALA 4.1 1.0 - - - -
38K ILE* 1.3 75.5 - - - +
40K ILE* 1.3 65.1 + - - +
47K CYS 3.6 2.0 - - - -
48K LEU* 3.6 24.2 - - - +
142K LEU* 4.5 3.3 - - - +
153K LEU* 3.4 17.0 - - - -
167K ALA* 3.2 21.5 - - - +
168K ARG 2.9 13.8 + - - -
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Residues in contact with ILE 40 (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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38K ILE* 4.8 11.9 - - + +
39K GLY* 1.3 79.5 - - - +
41K GLN* 1.3 70.8 + - - +
42K THR* 4.0 3.3 + - - +
46K VAL* 3.5 6.6 - - - +
47K CYS* 2.7 45.4 + - - +
153K LEU* 3.4 4.6 - - - +
166K ASP 3.7 3.8 - - - -
167K ALA* 4.2 15.0 - - + -
181K LEU* 5.5 2.5 - - + -
185K TYR* 5.1 10.1 - - + -
189K MET* 5.7 5.2 - - + -
194K ALA* 3.7 45.3 - - + +
197K SER* 4.8 5.8 - - - -
198K SER* 4.5 16.2 - - - +
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Residues in contact with GLN 41 (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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40K ILE* 1.3 80.2 - - - +
42K THR* 1.3 66.0 + - - +
45K GLY 4.3 1.6 - - - -
46K VAL* 4.7 2.0 - - + -
151K PRO 2.8 23.3 + - - +
152K GLN* 2.5 32.1 + - - +
153K LEU* 3.1 38.0 + - + +
164K GLN* 4.4 5.3 + - - +
165K CYS 3.8 5.5 - - - +
166K ASP* 2.9 33.0 + - + +
185K TYR* 4.5 14.9 + - - -
189K MET* 5.7 2.4 - - - +
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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