Contacts of the helix formed by residues 347 - 355 (chain Q) in PDB entry 5GJQ
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 ILE 347 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345Q VAL 3.1 3.3 + - - +
346Q GLN* 1.3 72.5 - - - +
348Q GLU* 1.3 85.4 + - - +
349Q HIS 3.0 0.3 + - - -
350Q ILE* 3.1 21.2 + - + -
351Q SER* 3.0 19.9 + - - -
358Q LYS* 5.3 5.2 - - + +
361Q VAL* 4.4 13.5 - - + -
362Q GLU* 3.5 50.5 - - + +
365Q LEU* 4.5 4.5 - - + -
378Q LEU* 3.9 19.1 - - + -
383Q GLY* 2.8 27.6 + - - +
384Q VAL 4.9 5.2 - - - +
385Q LEU* 5.0 1.6 - - + +
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Residues in contact with GLU 348 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346Q GLN* 3.1 8.0 + - + +
347Q ILE* 1.3 100.1 - - + +
349Q HIS* 1.3 56.8 + - - +
351Q SER* 3.3 7.8 - - - -
352Q SER* 3.1 27.7 + - - -
358Q LYS* 3.7 23.4 - - - +
362Q GLU* 5.2 0.9 - - - +
383Q GLY* 4.6 7.1 - - - +
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Residues in contact with HIS 349 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390P GLU* 3.8 8.8 + - - +
408P ARG* 3.1 51.8 + - + -
338Q VAL* 5.9 2.7 - - + -
345Q VAL* 4.2 9.4 - - + -
346Q GLN* 2.8 27.6 + - + +
348Q GLU* 1.3 75.3 - - - +
350Q ILE* 1.3 66.3 + - - +
351Q SER 3.0 1.1 + - - -
352Q SER* 3.3 9.7 + - - -
353Q LEU* 2.9 47.6 + - + +
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Residues in contact with ILE 350 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335Q LEU* 3.5 31.9 - - + -
338Q VAL* 3.7 30.2 - - + +
339Q ILE* 4.2 11.2 - - + -
345Q VAL* 3.5 45.5 - - + +
347Q ILE* 3.1 24.1 + - + +
349Q HIS* 1.3 76.4 - - - +
351Q SER* 1.3 67.3 + - - +
353Q LEU* 3.8 0.7 - - - +
354Q ILE* 2.9 25.1 + - + +
361Q VAL* 4.0 14.4 - - + -
365Q LEU* 4.7 2.9 - - + -
385Q LEU* 4.3 9.4 - - + -
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Residues in contact with SER 351 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347Q ILE 3.0 12.1 + - - -
348Q GLU* 3.3 15.0 - - - -
349Q HIS 3.0 0.2 - - - -
350Q ILE* 1.3 80.2 - - - +
352Q SER* 1.3 54.1 + - - +
354Q ILE* 3.1 7.6 - - - +
355Q LYS 2.5 34.0 + - - -
356Q LEU 2.2 33.7 + - - -
357Q SER* 4.3 0.7 - - - -
358Q LYS* 3.8 21.1 + - - -
361Q VAL* 4.5 5.3 - - - +
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Residues in contact with SER 352 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348Q GLU 3.1 10.5 + - - -
349Q HIS* 3.4 16.1 + - - -
351Q SER* 1.3 81.0 + - - +
353Q LEU* 1.3 64.6 + - - +
355Q LYS* 3.3 13.4 + - - +
356Q LEU 5.1 0.2 - - - +
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Residues in contact with LEU 353 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334Q ASN* 5.8 0.4 - - - -
338Q VAL* 4.5 15.7 - - + -
349Q HIS* 2.9 49.1 + - + +
350Q ILE* 3.8 3.8 - - - +
352Q SER* 1.3 80.1 - - - +
354Q ILE* 1.3 62.2 + - - +
355Q LYS* 3.1 3.8 + - - +
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Residues in contact with ILE 354 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299Q LEU* 3.6 34.0 - - + +
300Q ALA* 5.5 1.8 + - - +
331Q LEU* 5.5 1.3 - - + -
334Q ASN* 1.8 53.6 - - + +
335Q LEU* 4.9 7.6 - - + -
338Q VAL* 5.2 2.5 - - + +
350Q ILE* 2.9 23.3 + - + +
351Q SER* 3.1 18.6 - - - +
353Q LEU* 1.3 71.2 - - - +
355Q LYS* 1.3 72.4 + - - +
356Q LEU* 3.8 24.1 - - + +
361Q VAL* 4.2 10.8 - - + -
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Residues in contact with LYS 355 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Q ALA* 6.4 1.8 - - + -
351Q SER 2.5 14.9 + - - -
352Q SER* 3.3 11.6 + - - +
353Q LEU 3.0 7.7 - - - +
354Q ILE* 1.3 80.4 - - - +
356Q LEU* 1.3 62.6 + - - +
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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