Contacts of the helix formed by residues 337 - 345 (chain K) in PDB entry 6LTJ
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 TYR 337 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K LYS* 3.8 22.7 - - + -
27K PRO* 3.5 39.7 - - + -
30K VAL* 4.8 11.9 - - + +
334K GLU* 3.1 18.7 + - + +
336K LYS* 1.3 129.3 + - + +
338K SER* 1.3 59.7 + - - +
339K VAL 3.3 2.0 - - - -
340K TRP* 3.0 13.8 + - + +
341K ILE* 2.8 29.4 + - + +
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Residues in contact with SER 338 (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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141K SER* 4.3 9.9 - - - -
144K ALA* 3.5 16.0 - - - +
300K SER* 4.4 3.1 - - - -
332K PRO* 5.7 6.1 - - - -
334K GLU* 3.5 12.6 + - - -
335K ARG* 3.0 34.4 + - - +
336K LYS 3.6 1.0 - - - -
337K TYR* 1.3 75.9 - - - +
339K VAL* 1.3 58.1 + - - +
341K ILE* 2.9 12.2 + - - +
342K GLY* 2.4 34.5 + - - -
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Residues in contact with VAL 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K ASP* 4.2 13.9 - - + +
106K THR* 4.8 5.5 - - + +
137K GLN* 3.4 47.8 - - + +
140K LEU* 3.7 12.7 - - + +
141K SER* 3.9 25.1 - - - +
154K ASP* 5.2 5.8 - - - +
300K SER* 4.9 6.5 - - - -
301K GLY* 5.6 3.8 - - - +
335K ARG 5.3 2.0 - - - +
336K LYS 6.2 0.9 - - - +
337K TYR 3.3 0.8 - - - -
338K SER* 1.3 78.6 + - - +
340K TRP* 1.3 62.5 + - - +
342K GLY* 3.0 11.4 + - - +
343K GLY* 3.1 9.5 + - - -
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Residues in contact with TRP 340 (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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9K VAL* 3.4 24.0 - - + +
10K VAL 6.1 0.4 - - - -
11K ASP* 5.9 5.9 - - + +
18K LYS* 4.4 12.3 - - + +
19K ALA* 3.2 21.5 - - - -
20K GLY* 3.0 23.2 - - - +
21K PHE 3.6 2.5 - - - -
24K ASP* 3.2 38.4 - - + -
25K ASP 3.4 20.9 - - - -
26K ALA 3.3 17.7 - - - -
27K PRO* 3.4 38.4 - - + -
106K THR* 6.4 0.4 - - - -
337K TYR* 3.0 16.2 + - - +
339K VAL* 1.3 79.1 - - - +
341K ILE* 1.3 80.0 - - + +
343K GLY* 3.0 4.3 + - - -
344K SER* 2.4 46.5 + - - -
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Residues in contact with ILE 341 (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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25K ASP* 3.5 31.9 - - + +
27K PRO* 5.7 0.4 - - + -
144K ALA* 3.7 22.9 - - + +
334K GLU* 4.5 11.2 - - + +
337K TYR* 2.8 21.3 + - + +
338K SER* 3.1 11.2 - - - +
340K TRP* 1.3 87.2 - - + +
342K GLY* 1.3 57.4 + - - +
344K SER* 3.0 19.8 + - - -
345K ILE* 3.6 25.2 + - + +
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Residues in contact with GLY 342 (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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140K LEU* 3.2 40.8 - - - +
143K TYR* 4.3 6.1 - - - +
144K ALA* 4.0 9.0 - - - -
338K SER 2.4 20.2 + - - -
339K VAL 3.0 7.3 + - - -
341K ILE* 1.3 68.8 - - - +
343K GLY* 1.3 55.8 + - - +
345K ILE* 5.1 1.6 - - - +
346K LEU* 3.2 19.1 + - - +
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Residues in contact with GLY 343 (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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9K VAL* 3.8 18.4 - - - -
104K LEU* 4.7 0.9 - - - -
140K LEU* 3.6 13.9 - - - +
339K VAL 3.1 5.1 + - - -
340K TRP 3.0 7.4 + - - -
342K GLY* 1.3 77.2 - - - +
344K SER* 1.3 57.0 + - - +
345K ILE 3.1 4.7 - - - -
346K LEU* 2.9 7.5 + - - -
347K ALA* 2.8 35.9 + - - +
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Residues in contact with SER 344 (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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9K VAL* 3.5 2.6 - - - +
21K PHE 3.4 6.8 + - - -
22K ALA* 3.2 28.0 - - - +
23K GLY 3.3 8.7 + - - -
24K ASP 3.5 20.5 - - - +
25K ASP* 4.7 0.5 - - - +
340K TRP* 2.4 49.1 + - - -
341K ILE* 3.0 12.0 + - - -
343K GLY* 1.3 76.6 - - - +
345K ILE* 1.3 63.4 + - - +
348K SER* 5.2 0.5 - - - -
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Residues in contact with ILE 345 (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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507I TYR* 3.5 35.8 - - + +
508I HIS* 3.6 34.8 - - + +
511I THR* 5.8 3.4 - - + +
25K ASP* 5.0 9.2 - - - +
143K TYR* 4.5 7.6 - - + +
144K ALA* 5.3 4.9 - - - +
341K ILE* 3.6 22.0 + - + +
342K GLY* 5.1 2.2 - - - +
344K SER* 1.3 81.8 - - - +
346K LEU* 1.3 69.7 + - + +
347K ALA 3.3 1.6 - - - -
348K SER* 2.8 29.7 + - - -
349K LEU* 3.8 1.9 + - - +
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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