Contacts of the helix formed by residues 341 - 355 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A ILE* 3.4 18.7 - - - +
340A PRO* 1.3 81.2 - - + +
342A ALA* 1.3 59.1 + - - +
344A GLU* 3.2 25.4 + - + +
345A ARG* 2.8 44.7 + - - +
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Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A VAL* 3.4 26.6 + - + +
160A GLY 3.8 3.6 - - - +
161A ASN* 3.2 40.6 - - - +
162A PRO* 3.6 4.7 - - + -
339A ILE 4.3 4.1 + - - +
340A PRO 3.6 4.0 + - - -
341A ASP* 1.3 74.8 + - - +
343A THR* 1.3 65.0 + - - +
345A ARG* 3.1 4.1 + - - +
346A VAL* 2.9 29.7 + - + +
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Residues in contact with THR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 3.7 33.9 - - + +
26A VAL* 4.2 9.2 - - - +
29A HIS* 3.8 22.2 - - + +
162A PRO* 3.2 30.8 - - - +
163A VAL 4.9 1.6 + - - -
341A ASP 3.4 0.4 - - - -
342A ALA* 1.3 77.5 - - - +
344A GLU* 1.3 66.0 + - - +
346A VAL* 4.0 1.0 - - - +
347A ALA* 2.9 31.4 + - - +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 3.5 33.3 - - + +
340A PRO 4.1 4.0 - - - +
341A ASP* 3.2 33.3 - - + +
343A THR* 1.3 81.6 + - - +
345A ARG* 1.3 55.2 + - - +
347A ALA* 3.6 0.9 - - - +
348A ASN* 2.6 47.9 + - - +
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Residues in contact with ARG 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A MET* 5.4 0.9 - - - -
157A GLU* 3.1 28.5 + - - +
158A VAL 2.9 28.8 + - - -
159A VAL* 3.1 33.0 - - + +
339A ILE* 3.9 18.4 - - - +
341A ASP* 2.8 33.2 + - - +
342A ALA* 3.1 5.8 + - - +
344A GLU* 1.3 74.2 - - - +
346A VAL* 1.3 65.6 + - - +
348A ASN* 3.2 10.5 + - - +
349A GLU* 3.0 26.5 + - + +
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 4.0 21.8 - - + -
101A LEU* 4.1 22.2 - - + -
103A MET* 5.5 1.1 - - + -
125A HIS* 3.8 30.5 - - + +
146A MET* 3.8 24.7 - - + -
159A VAL* 3.8 15.5 - - + -
160A GLY 5.5 0.2 - - - +
162A PRO* 6.1 2.5 - - + -
342A ALA* 2.9 21.6 + - + +
343A THR 4.1 2.2 - - - +
345A ARG* 1.3 72.1 - - - +
347A ALA* 1.3 58.5 + - - +
349A GLU* 3.2 2.3 + - - +
350A VAL* 2.9 30.8 + - + +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 4.2 14.3 - - + +
29A HIS* 3.5 29.8 - - + -
30A LEU* 3.8 20.3 - - + +
343A THR 2.9 20.5 + - - +
344A GLU 3.6 3.1 - - - +
346A VAL* 1.3 77.6 - - - +
348A ASN* 1.3 58.7 + - - +
350A VAL* 3.3 5.2 + - - +
351A SER* 3.0 27.0 + - - -
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Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 5.7 1.6 + - - -
344A GLU* 2.6 38.2 + - - +
345A ARG* 3.5 9.0 - - - +
347A ALA* 1.3 75.7 - - - +
349A GLU* 1.3 61.7 + - + +
351A SER* 3.2 9.1 + - - -
352A ARG* 2.8 30.0 + - - +
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Residues in contact with GLU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 5.2 0.7 - - - -
144A LYS* 3.6 22.6 + - + +
146A MET* 3.6 39.5 - - + -
157A GLU* 4.1 12.7 - - - +
345A ARG* 3.0 15.2 + - + +
346A VAL 3.7 2.0 - - - +
348A ASN* 1.3 74.4 - - + +
350A VAL* 1.3 66.0 + - - +
352A ARG* 2.7 52.8 + - - +
353A VAL* 2.9 30.5 + - - +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.9 11.2 - - + -
26A VAL* 4.8 2.5 - - + -
30A LEU* 4.0 10.8 - - + -
35A TRP* 3.9 11.0 - - + -
99A VAL* 3.8 24.5 - - + +
101A LEU* 3.8 31.9 - - + -
123A VAL* 4.1 20.4 - - + -
346A VAL* 2.9 22.5 + - + +
347A ALA* 3.5 10.3 - - - +
348A ASN 3.2 0.2 - - - -
349A GLU* 1.3 77.9 - - - +
351A SER* 1.3 56.8 + - - +
353A VAL* 3.4 1.9 + - - +
354A ALA* 2.9 28.2 + - - +
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Residues in contact with SER 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.3 3.1 - - - -
35A TRP* 3.7 22.7 + - - -
347A ALA 3.0 13.4 + - - -
348A ASN* 3.2 12.1 + - - -
350A VAL* 1.3 79.3 - - - +
352A ARG* 1.3 62.4 + - - +
354A ALA* 3.5 2.1 + - - +
355A ARG* 3.2 50.8 + - - +
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Residues in contact with ARG 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR 5.7 0.6 + - - -
144A LYS* 4.2 15.8 - - - +
348A ASN 2.8 16.2 + - - +
349A GLU* 2.7 41.7 + - - +
350A VAL 3.3 0.2 - - - -
351A SER* 1.3 76.6 - - - +
353A VAL* 1.3 70.5 + - - +
355A ARG* 3.3 3.2 + - - +
356A ALA 3.3 3.5 + - - -
357A LEU* 3.0 70.3 + - + +
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Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 4.1 1.8 - - + -
121A PRO* 3.3 39.2 - - + +
123A VAL* 3.8 26.7 - - + -
143A THR* 4.0 18.4 - - + -
144A LYS* 4.1 18.6 - - + -
349A GLU 2.9 21.2 + - - +
350A VAL 3.8 2.7 - - - +
352A ARG* 1.3 85.8 - - - +
354A ALA* 1.3 60.7 + - - +
355A ARG 3.0 1.8 - - - -
356A ALA* 2.8 22.7 + - - +
357A LEU 4.8 1.1 - - - +
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Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS* 3.1 25.5 + - + +
35A TRP* 3.6 14.1 - - + -
98A ASP* 4.1 16.2 - - + +
99A VAL* 3.6 28.7 - - + -
121A PRO* 5.4 0.5 - - - +
350A VAL 2.9 18.3 + - - +
351A SER 3.8 2.5 - - - +
353A VAL* 1.3 77.9 - - - +
355A ARG* 1.3 58.9 + - - +
356A ALA* 3.5 2.1 + - - +
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Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS* 3.5 37.9 - - - +
35A TRP* 4.7 6.5 - - - +
351A SER* 3.2 36.0 + - - +
352A ARG 3.7 4.7 - - - +
353A VAL 3.0 0.6 - - - -
354A ALA* 1.3 75.9 - - - +
356A ALA* 1.3 69.2 - - - +
357A LEU* 3.4 25.0 + - + +
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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