Contacts of the helix formed by residues 348 - 354 (chain A) in PDB entry 5FLM
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 GLY 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A GLN 5.1 2.2 - - - -
342A ARG 3.2 17.5 - - - -
343A LEU 4.9 1.1 - - - -
344A LYS 4.6 3.6 - - - -
345A GLY 2.7 19.7 + - - -
346A LYS 3.1 1.8 + - - -
347A GLU* 1.3 80.2 - - - +
349A ARG* 1.3 61.9 + - - -
350A VAL 3.1 3.2 + - - -
351A ARG 3.2 1.5 + - - -
352A GLY* 2.4 34.2 + - - -
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Residues in contact with ARG 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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337A LYS* 5.7 3.0 - - - +
342A ARG* 3.1 31.1 + - - +
343A LEU* 3.6 18.5 - - + +
347A GLU 4.2 9.5 + - - -
348A GLY* 1.3 70.4 - - - -
350A VAL* 1.3 63.4 + - - +
353A ASN* 2.9 45.2 + - + -
354A LEU* 3.0 16.3 + - - +
1070B LEU* 3.3 31.6 - - - +
1071B ASN* 4.2 2.4 + - - +
1154B ALA* 5.0 9.0 - - - +
1157B LEU* 3.4 28.7 - - + +
1158B LEU* 4.7 7.0 - - + -
1161B GLU* 3.2 29.6 + - - +
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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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343A LEU* 3.7 24.0 - - + +
344A LYS 5.5 0.2 - - - +
348A GLY 3.2 1.0 - - - -
349A ARG* 1.3 78.1 - - - +
351A ARG* 1.3 63.8 + - + +
354A LEU* 3.2 10.2 - - - +
355A MET* 3.1 22.8 + - + +
1430A CYS* 3.8 18.6 - - + +
1431A SER* 3.6 35.7 - - - +
1435A THR* 5.3 5.4 - - + -
1439A LEU* 5.7 4.5 - - + -
1459A MET* 4.5 11.4 - - + -
1158B LEU* 3.9 27.1 - - + -
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Residues in contact with ARG 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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344A LYS 4.9 5.9 + - - +
345A GLY* 4.3 11.9 + - - +
346A LYS* 3.7 46.2 - - + +
348A GLY 3.2 1.8 + - - -
350A VAL* 1.3 83.8 - - + +
352A GLY* 1.3 63.1 + - - +
355A MET* 4.0 9.4 - - - +
356A GLY 3.8 12.0 + - - -
862A ARG* 2.9 42.8 - - - +
1431A SER 4.5 6.2 + - - +
1433A GLU* 4.0 21.6 - - - +
1435A THR* 6.1 3.1 - - + +
1085B ARG* 3.6 10.4 + - - +
1088B GLU* 3.2 26.0 - - + +
14T T 5.6 0.6 + - - -
15T A 4.0 24.2 + - - -
17T G 5.4 4.6 + - - -
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Residues in contact with GLY 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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346A LYS* 5.9 0.2 - - - -
347A GLU* 3.6 24.7 - - - +
348A GLY 2.4 24.7 + - - -
351A ARG* 1.3 70.6 - - - +
353A ASN* 1.3 59.1 + - - -
356A GLY 2.6 19.8 - - - +
357A LYS* 4.3 0.3 - - - -
1085B ARG* 3.0 25.9 + - - -
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Residues in contact with ASN 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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347A GLU 4.5 4.6 + - - +
348A GLY 3.5 0.4 + - - -
349A ARG* 2.9 41.7 + - - +
352A GLY* 1.3 78.4 + - - -
354A LEU* 1.3 58.2 + - - +
356A GLY 3.5 7.0 - - - -
357A LYS* 3.5 7.1 - - - -
358A ARG* 5.1 6.5 - - - +
1071B ASN* 2.9 41.7 + - - +
1073B GLN* 3.1 35.8 + - - +
1085B ARG* 5.5 1.2 - - - +
1154B ALA* 3.3 22.8 - - + +
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Residues in contact with LEU 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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349A ARG 3.0 15.9 + - - +
350A VAL* 3.2 13.2 + - - +
352A GLY 3.6 0.8 - - - -
353A ASN* 1.3 77.9 - - - +
355A MET* 1.3 69.5 + - - +
356A GLY 3.1 2.0 + - - -
357A LYS* 3.8 12.2 + - - +
1458A ILE* 5.5 2.4 - - - +
1459A MET* 3.8 35.5 - - + +
1107B LEU* 3.7 14.4 - - - +
1152B PRO* 5.0 5.8 - - + -
1154B ALA* 3.6 12.3 - - + +
1155B CYS* 3.4 36.8 - - + +
1158B LEU* 3.5 38.1 - - + -
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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