Contacts of the helix formed by residues 341 - 355 (chain B) in PDB entry 1F0K
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 ASP 341 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B ILE* 4.0 7.6 - - - +
340B PRO* 1.3 83.9 - - + +
342B ALA* 1.3 63.6 + - - +
343B THR 3.2 2.9 - - - -
344B GLU* 3.2 29.0 + - + +
345B ARG* 2.9 50.8 + - - +
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B VAL 3.0 28.2 + - - +
160B GLY 3.5 7.6 - - - +
161B ASN 3.3 35.9 - - - +
162B PRO* 3.7 2.2 - - + +
339B ILE* 3.8 6.5 + - - +
340B PRO 3.5 4.0 + - - -
341B ASP* 1.3 75.3 + - - +
343B THR* 1.3 64.4 + - - +
345B ARG* 3.3 3.8 + - - +
346B VAL* 3.0 30.8 + - + +
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA* 3.6 32.8 - - + +
26B VAL* 4.2 6.3 - - - +
29B HIS* 3.9 20.9 - - + +
162B PRO* 3.0 33.8 - - - +
163B VAL 4.8 1.2 + - - -
341B ASP 3.2 0.6 - - - -
342B ALA* 1.3 79.5 - - - +
344B GLU* 1.3 70.8 + - - +
346B VAL* 3.3 4.4 + - - +
347B ALA* 3.0 22.2 + - - +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B HIS* 3.4 34.4 - - + +
340B PRO 4.6 2.0 - - - +
341B ASP* 3.2 35.9 + - + +
343B THR* 1.3 82.1 - - - +
345B ARG* 1.3 57.9 + - - +
347B ALA* 3.3 0.9 + - - +
348B ASN* 2.8 45.3 + - - +
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Residues in contact with ARG 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B MET* 4.8 1.6 - - - -
157B GLU* 4.9 9.0 + - - +
158B VAL 3.5 22.2 + - - -
159B VAL* 4.1 26.1 - - + +
339B ILE* 4.1 22.2 - - - +
341B ASP* 2.9 43.7 + - - +
342B ALA 3.6 4.0 - - - +
344B GLU* 1.3 76.7 - - - +
346B VAL* 1.3 61.7 + - - +
348B ASN* 3.4 8.1 + - - +
349B GLU* 3.1 28.3 + - + +
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 3.9 24.9 - - + -
101B LEU* 4.6 11.7 - - + -
103B MET* 5.3 1.1 - - + -
125B HIS* 3.9 30.5 - - + +
146B MET* 3.9 21.5 - - + -
159B VAL* 3.9 14.6 - - + -
162B PRO* 6.0 2.7 - - + -
342B ALA* 3.0 18.8 + - + +
343B THR* 3.8 2.9 - - - +
345B ARG* 1.3 74.4 - - - +
347B ALA* 1.3 58.7 + - - +
349B GLU* 3.2 3.3 + - - +
350B VAL* 2.9 42.3 + - + +
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 4.3 13.8 - - + +
29B HIS* 3.5 29.4 - - + -
30B LEU* 3.8 25.1 - - + +
343B THR 3.0 17.3 + - - +
344B GLU 3.7 2.2 - - - +
346B VAL* 1.3 77.2 - - - +
348B ASN* 1.3 59.3 + - - +
350B VAL* 3.4 4.8 + - - +
351B SER* 2.9 29.2 + - - -
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Residues in contact with ASN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B HIS* 5.3 3.5 + - - -
344B GLU* 2.8 34.0 + - - +
345B ARG* 3.7 7.0 - - - +
347B ALA* 1.3 77.3 - - - +
349B GLU* 1.3 58.4 + - + +
351B SER* 3.3 8.1 + - - -
352B ARG* 2.9 28.1 + - - +
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Residues in contact with GLU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B VAL* 5.2 0.7 - - - -
144B LYS* 3.4 21.2 - - + +
146B MET* 3.7 28.3 - - + -
157B GLU* 4.2 11.6 - - - +
159B VAL* 6.0 0.2 - - + -
345B ARG 3.1 18.8 + - - +
346B VAL 3.7 4.0 - - - +
348B ASN* 1.3 75.1 - - + +
350B VAL* 1.3 61.4 + - - +
352B ARG* 2.8 54.5 + - - +
353B VAL* 2.9 36.2 + - - +
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.0 13.9 - - + -
26B VAL* 4.9 2.0 - - + -
30B LEU* 4.0 14.8 - - + -
35B TRP* 4.5 3.4 - - + -
99B VAL* 3.7 26.1 - - + +
101B LEU* 3.9 26.9 - - + -
123B VAL* 4.0 23.1 - - + -
346B VAL* 2.9 27.3 + - + +
347B ALA* 3.6 8.1 - - - +
349B GLU* 1.3 76.1 - - - +
351B SER* 1.3 62.5 + - - +
353B VAL* 4.0 1.0 - - - +
354B ALA* 3.1 22.9 + - - +
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Residues in contact with SER 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LYS* 4.2 0.2 + - - -
30B LEU* 5.0 3.6 - - - -
35B TRP* 4.0 23.8 + - - -
347B ALA 2.9 17.3 + - - -
348B ASN* 3.5 9.9 - - - -
349B GLU 3.1 0.2 - - - -
350B VAL* 1.3 76.5 - - - +
352B ARG* 1.3 56.8 + - - +
354B ALA* 3.4 2.9 + - - +
355B ARG* 2.7 55.9 + - - +
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Residues in contact with ARG 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B THR* 5.3 4.4 + - - +
144B LYS* 4.0 16.6 - - - +
348B ASN 2.9 17.6 + - - +
349B GLU* 2.8 39.5 + - - +
351B SER* 1.3 77.9 - - - +
353B VAL* 1.3 73.3 + - - +
355B ARG* 3.2 9.3 + - - +
356B ALA 3.2 3.5 + - - -
357B LEU* 3.1 60.3 + - + -
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 4.3 1.1 - - + -
121B PRO* 3.3 36.2 - - + +
123B VAL* 3.8 22.0 - - + -
143B THR* 3.9 17.9 - - + -
144B LYS* 3.9 19.1 - - + -
349B GLU* 2.9 22.2 + - - +
350B VAL 4.1 1.6 - - - +
352B ARG* 1.3 96.0 - - - +
354B ALA* 1.3 62.3 + - - +
355B ARG 3.1 1.1 - - - -
356B ALA* 3.0 19.9 + - - +
357B LEU 4.9 1.1 - - - +
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Residues in contact with ALA 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LYS* 3.9 13.2 + - + +
35B TRP* 3.6 23.1 - - + -
98B ASP* 4.1 25.5 - - + +
99B VAL* 3.9 13.4 - - + +
121B PRO* 4.7 0.4 - - - +
350B VAL 3.1 19.2 + - - +
351B SER 3.7 3.4 - - - +
352B ARG 3.3 0.2 - - - -
353B VAL* 1.3 75.6 - - - +
355B ARG* 1.3 60.4 + - - +
356B ALA* 3.0 5.8 + - - +
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Residues in contact with ARG 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 2.8 40.1 - - - +
35B TRP* 5.4 4.6 - - - +
351B SER* 2.7 37.5 + - - +
352B ARG* 3.3 11.7 - - - +
353B VAL 3.1 0.2 - - - -
354B ALA* 1.3 75.9 - - - +
356B ALA* 1.3 69.1 + - - +
357B LEU* 3.2 29.5 + - + +
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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