Contacts of the helix formed by residues 53 - 61 (chain L) in PDB entry 6AHU
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 SER 53 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49L CYS* 5.4 0.6 - - - -
51L ILE 3.8 2.0 + - - -
52L LEU* 1.3 83.3 - - - +
54L GLU* 1.3 63.7 + - - +
55L GLU* 4.3 5.6 - - - +
56L LEU* 3.5 24.1 + - - +
57L LYS* 3.2 17.5 + - - +
296L HIS* 4.3 6.6 + - - -
300L TYR* 5.6 9.3 - - - -
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Residues in contact with GLU 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L LEU 4.8 4.7 - - - +
53L SER* 1.3 71.1 - - - +
55L GLU* 1.3 62.1 + - - +
56L LEU 3.4 0.2 - - - -
57L LYS* 3.9 14.3 - - + +
58L ASN* 2.9 36.5 + - - +
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Residues in contact with GLU 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L SER* 3.2 4.6 - - - +
54L GLU* 1.3 79.3 - - - +
56L LEU* 1.3 61.3 + - - +
58L ASN* 3.6 7.2 + - - +
59L LEU* 3.4 19.2 + - - +
296L HIS* 3.6 28.9 + - + +
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Residues in contact with LEU 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L PHE* 3.8 28.0 - - + -
46L ILE* 4.6 8.7 - - + -
52L LEU* 3.8 23.6 - - + -
53L SER* 3.4 21.7 + - - +
55L GLU* 1.3 75.7 - - - +
57L LYS* 1.3 64.4 + - - +
59L LEU* 3.1 19.2 + - + +
60L VAL* 3.2 16.1 + - + +
293L LEU* 3.8 27.6 - - + -
296L HIS* 3.5 30.4 + - + +
297L LEU* 4.9 8.5 - - + -
300L TYR* 5.8 7.0 - - + -
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Residues in contact with LYS 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L LEU* 3.5 40.5 - - + +
53L SER 3.2 14.2 + - - +
54L GLU* 4.0 12.8 - - + +
55L GLU 3.3 0.4 - - - -
56L LEU* 1.3 78.8 - - - +
58L ASN* 1.3 62.5 + - - +
59L LEU 3.5 0.3 + - - -
60L VAL* 3.6 6.2 + - + +
61L MET* 3.6 31.2 + - + +
211L LEU* 4.2 22.1 - - + +
277L TYR* 4.2 3.2 + - - -
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Residues in contact with ASN 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L GLU* 2.9 25.3 + - - +
55L GLU* 4.0 6.9 - - - +
56L LEU 3.3 0.6 - - - -
57L LYS* 1.3 78.4 - - - +
59L LEU* 1.3 61.6 + - - +
60L VAL 3.4 0.2 - - - -
61L MET* 3.8 4.9 + - - +
62L ASN* 2.9 38.7 + - - +
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Residues in contact with LEU 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L GLU 3.4 11.5 + - - +
56L LEU* 3.1 18.9 + - + +
58L ASN* 1.3 77.5 - - - +
60L VAL* 1.3 64.2 + - - +
61L MET 3.4 0.2 - - - -
62L ASN* 3.5 14.7 + - + +
63L THR* 3.4 17.1 - - + +
289L LYS* 4.9 10.3 - - + +
292L LEU* 3.8 45.3 - - + +
293L LEU* 3.8 30.3 - - + -
296L HIS* 4.4 9.0 - - + -
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Residues in contact with VAL 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L PHE* 3.6 33.2 - - + -
52L LEU* 5.7 3.1 - - + -
56L LEU* 3.2 19.5 + - + +
57L LYS* 3.6 8.0 + - - +
58L ASN 3.4 0.2 - - - -
59L LEU* 1.3 78.6 - - + +
61L MET* 1.3 63.5 + - + +
62L ASN 3.2 1.1 + - - -
63L THR* 3.3 23.0 + - - +
209L VAL* 3.8 32.9 - - + +
211L LEU* 4.9 4.3 - - + -
279L CYS* 4.1 6.1 - - - -
281L ILE* 3.8 26.4 - - + +
293L LEU* 5.6 1.6 - - + -
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Residues in contact with MET 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L LYS* 3.6 24.0 + - + +
58L ASN* 3.8 6.3 + - - +
59L LEU 3.4 0.4 - - - -
60L VAL* 1.3 76.3 - - + +
62L ASN* 1.3 68.3 + - - +
63L THR* 3.6 1.7 + - - -
64L GLY 5.4 0.5 + - - -
206L GLN* 4.7 10.4 - - - +
207L PRO* 6.0 1.4 - - - +
209L VAL* 3.8 37.9 - - + -
211L LEU* 4.4 14.8 - - + -
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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