Contacts of the helix formed by residues 51 - 63 (chain B) in PDB entry 1AHF
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 THR 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B VAL 4.5 2.7 - - - +
50B LEU* 1.3 68.4 - - - +
52B SER* 1.3 62.0 + - - +
53B VAL 3.1 2.0 - - - -
54B LYS* 3.3 8.3 + - - +
55B LYS* 2.8 39.0 + - - +
318B ILE* 4.7 8.7 - - - +
322B GLU* 3.0 18.2 + - - +
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Residues in contact with SER 52 (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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50B LEU* 3.7 8.8 - - - +
51B THR* 1.3 77.6 + - - +
53B VAL* 1.3 59.0 + - - +
55B LYS* 3.2 5.3 - - - +
56B ALA* 2.9 27.4 + - - +
309B ILE* 3.7 13.5 - - - +
315B LEU* 3.9 19.1 - - - +
318B ILE* 4.2 5.3 - - - +
319B TRP* 3.5 37.2 - - - +
322B GLU* 2.9 20.1 + - - -
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Residues in contact with VAL 53 (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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68A LYS* 4.5 0.9 - - + -
49B VAL* 3.4 23.1 - - + -
50B LEU* 3.5 19.2 + - + +
51B THR 3.1 0.2 - - - -
52B SER* 1.3 79.1 + - - +
54B LYS* 1.3 53.9 + - - +
56B ALA* 2.9 3.6 + - - +
57B GLU* 2.8 54.1 + - + +
260B PHE* 3.6 26.5 - - + +
262B LEU* 4.1 20.9 - - + -
305B VAL* 4.1 15.7 - - + +
309B ILE* 4.0 13.5 - - + -
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Residues in contact with LYS 54 (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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60A LEU 4.0 0.2 + - - -
61A LEU* 2.8 40.9 + - + +
62A GLU 4.9 0.8 + - - -
63A ASN 4.8 0.2 - - - -
64A GLU* 2.7 43.1 + - - +
49B VAL* 3.8 22.7 - - + +
50B LEU 3.3 11.5 + - - +
51B THR* 3.3 12.0 + - - +
53B VAL* 1.3 75.0 - - - +
55B LYS* 1.3 68.9 + - - +
57B GLU* 3.3 18.3 + - - +
58B GLN* 3.1 21.5 + - - +
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Residues in contact with LYS 55 (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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51B THR* 2.8 25.0 + - - +
52B SER* 3.2 11.2 - - - +
54B LYS* 1.3 80.0 - - + +
56B ALA* 1.3 62.2 + - - +
58B GLN* 3.2 21.5 + - - +
59B TYR* 3.3 11.8 + - - +
315B LEU* 3.9 22.9 - - + -
318B ILE* 5.5 10.1 - - + +
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Residues in contact with ALA 56 (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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52B SER 2.9 14.6 + - - +
53B VAL 2.9 6.9 + - - +
55B LYS* 1.3 77.3 - - - +
57B GLU* 1.3 56.2 + - - +
59B TYR* 3.2 10.3 + - - +
60B LEU* 2.8 32.7 + - - +
305B VAL* 3.9 29.8 - - + +
308B THR* 4.1 15.5 - - + -
309B ILE* 3.9 9.2 - - + -
315B LEU* 4.3 5.6 - - + +
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Residues in contact with GLU 57 (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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61A LEU* 4.4 17.3 - - + +
64A GLU* 4.1 4.8 - - - +
68A LYS* 2.8 28.5 + - - -
301A HIS* 4.9 1.4 - - - -
49B VAL* 4.4 1.0 - - - +
53B VAL* 2.8 33.6 + - + +
54B LYS* 3.7 24.4 + - - +
56B ALA* 1.3 71.8 - - - +
58B GLN* 1.3 55.7 + - - +
60B LEU* 3.2 7.5 + - - +
61B LEU* 2.7 35.6 + - - +
301B HIS* 2.6 37.0 + - + +
305B VAL* 3.8 11.2 - - + +
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Residues in contact with GLN 58 (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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58A GLN* 5.8 2.0 - - - +
61A LEU* 3.9 30.4 - - + +
54B LYS 3.1 12.1 + - - +
55B LYS* 3.4 19.5 - - - +
56B ALA 3.2 0.2 - - - -
57B GLU* 1.3 73.3 - - - +
59B TYR* 1.3 67.2 + - - +
61B LEU* 3.1 5.5 + - + +
62B GLU* 2.9 50.9 + - + +
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Residues in contact with TYR 59 (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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55B LYS 3.3 8.6 + - - +
56B ALA* 3.2 11.9 + - - +
58B GLN* 1.3 81.8 - - - +
60B LEU* 1.3 74.8 + - + +
62B GLU* 4.4 7.6 - - - -
63B ASN* 2.8 73.5 + - + +
308B THR* 4.1 21.8 - - + -
315B LEU* 6.2 0.9 - - + -
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Residues in contact with LEU 60 (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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56B ALA 2.8 16.5 + - - +
57B GLU* 3.7 6.1 - - - +
59B TYR* 1.3 92.6 - - + +
61B LEU* 1.3 60.7 + - - +
63B ASN* 4.4 0.4 - - + +
64B GLU* 2.8 60.1 + - + +
301B HIS* 4.2 13.9 - - + +
304B SER* 3.4 35.7 - - - +
305B VAL* 3.8 25.8 - - + +
308B THR* 4.3 9.0 - - - +
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Residues in contact with LEU 61 (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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54A LYS* 3.0 47.5 + - + +
57A GLU* 4.1 24.0 - - + +
58A GLN* 3.9 36.1 - - + +
61A LEU* 3.7 24.7 - - + -
57B GLU 2.7 17.5 + - - +
58B GLN* 3.1 13.0 - - + +
60B LEU* 1.3 74.0 - - - +
62B GLU* 1.3 62.6 + - + +
64B GLU* 5.8 0.7 - - - -
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Residues in contact with GLU 62 (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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54A LYS* 4.9 0.8 + - - -
58B GLN* 2.9 42.0 + - + +
59B TYR* 4.4 6.1 - - - -
61B LEU* 1.3 83.7 - - + +
63B ASN* 1.3 76.8 + - - +
64B GLU 4.9 0.9 - - - +
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Residues in contact with ASN 63 (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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59B TYR* 2.8 69.8 + - + +
60B LEU* 5.1 0.7 - - + -
62B GLU* 1.3 93.7 + - - +
64B GLU* 1.3 64.4 + - - +
66B THR* 3.2 15.8 + - - +
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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