Contacts of the helix formed by residues 51 - 63 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL 3.6 2.3 + - - -
50A LEU* 1.3 71.7 - - - +
52A SER* 1.3 54.1 - - - +
54A LYS* 3.0 9.7 + - + +
55A LYS* 2.8 53.3 + - + +
318A ILE* 4.7 10.8 - - + -
322A GLU* 2.9 19.1 + - - -
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Residues in contact with SER 52 (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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50A LEU* 3.8 8.7 - - - +
51A THR* 1.3 74.3 - - - +
53A VAL* 1.4 57.8 + - - +
55A LYS* 3.5 3.0 + - - +
56A ALA* 2.9 22.7 + - - +
309A ILE* 3.4 21.6 - - - +
315A LEU* 3.9 20.6 - - - +
318A ILE* 4.2 6.7 - - - +
319A TRP* 3.6 34.4 - - - +
322A GLU* 2.7 22.8 + - - -
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Residues in contact with VAL 53 (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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49A VAL* 3.4 24.7 - - + -
50A LEU* 3.2 19.0 + - + +
51A THR 3.1 0.8 - - - -
52A SER* 1.4 79.1 + - - +
54A LYS* 1.4 53.8 + - - +
56A ALA* 2.9 3.8 + - - +
57A GLU* 2.7 51.0 + - - +
260A PHE* 3.6 26.5 - - + +
262A LEU* 4.0 23.6 - - + -
305A VAL* 4.1 18.1 - - + +
309A ILE* 4.0 11.2 - - + -
68B LYS* 4.2 0.9 - - - -
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Residues in contact with LYS 54 (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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49A VAL* 3.9 25.6 - - + +
50A LEU 3.1 10.3 + - - +
51A THR* 3.0 10.1 + - + +
53A VAL* 1.4 72.5 - - - +
55A LYS* 1.3 66.5 + - + +
57A GLU* 3.0 26.0 + - - +
58A GLN* 3.0 14.9 + - - +
60B LEU 4.0 0.2 + - - -
61B LEU* 3.0 38.8 + - + +
62B GLU 4.9 0.4 - - - -
64B GLU* 2.5 46.9 + - - +
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Residues in contact with LYS 55 (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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51A THR* 2.8 34.0 + - + +
52A SER 3.7 4.9 - - - +
54A LYS* 1.3 77.0 - - + +
56A ALA* 1.3 62.5 + - - +
58A GLN* 3.3 6.4 + - - +
59A TYR* 3.2 21.7 + - - +
315A LEU* 3.8 23.6 - - + -
318A ILE* 4.4 17.5 - - + +
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Residues in contact with ALA 56 (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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52A SER 2.9 21.0 + - - +
53A VAL 2.9 3.8 + - - +
55A LYS* 1.3 73.3 - - - +
57A GLU* 1.3 57.4 + - - +
59A TYR* 3.3 9.8 - - - +
60A LEU* 3.0 32.0 + - - +
305A VAL* 4.0 21.1 - - + +
308A THR* 4.1 13.5 - - + -
309A ILE* 3.8 20.0 - - + -
315A LEU* 4.3 5.8 - - + +
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Residues in contact with GLU 57 (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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53A VAL* 2.7 28.5 + - - +
54A LYS* 3.0 24.7 + - - +
56A ALA* 1.3 72.1 - - - +
58A GLN* 1.3 60.6 + - - +
60A LEU* 3.3 6.6 + - - +
61A LEU* 2.9 27.5 + - - +
301A HIS* 2.8 40.4 + - + +
305A VAL* 3.8 9.9 - - + -
61B LEU* 4.1 17.7 - - + +
64B GLU* 4.0 4.7 - - - +
68B LYS* 2.9 35.2 + - - -
301B HIS* 5.0 0.9 + - - -
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Residues in contact with GLN 58 (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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54A LYS 3.0 11.4 + - - +
55A LYS* 3.3 10.3 + - - +
57A GLU* 1.3 72.6 - - - +
59A TYR* 1.3 67.9 + - - +
61A LEU* 3.0 9.4 + - + +
62A GLU* 2.9 53.9 + - - +
58B GLN* 5.8 2.0 - - - +
61B LEU* 3.9 29.7 - - + +
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Residues in contact with TYR 59 (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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55A LYS 3.2 9.7 + - - +
56A ALA* 3.3 12.6 - - - +
58A GLN* 1.3 81.9 - - - +
60A LEU* 1.3 78.1 + - + +
62A GLU* 4.7 4.0 - - - -
63A ASN* 2.9 63.8 + - + +
308A THR* 4.1 25.8 - - + -
315A LEU* 5.9 1.8 - - + -
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Residues in contact with LEU 60 (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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56A ALA 3.0 16.7 + - - +
57A GLU* 3.7 6.1 - - - +
58A GLN 3.2 0.2 - - - -
59A TYR* 1.3 90.8 - - + +
61A LEU* 1.3 61.3 + - - +
63A ASN* 4.3 0.9 - - + +
64A GLU* 2.7 58.8 + - + +
301A HIS* 4.1 17.5 - - + +
304A SER* 3.5 35.4 - - - +
305A VAL* 3.9 24.5 - - + +
308A THR* 4.2 9.4 - - - +
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Residues in contact with LEU 61 (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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57A GLU 2.9 15.0 + - - +
58A GLN* 3.1 17.5 - - - +
60A LEU* 1.3 75.4 - - - +
62A GLU* 1.3 61.6 + - + +
64A GLU* 5.8 0.4 - - - -
54B LYS* 2.8 57.2 + - + +
57B GLU* 4.4 15.5 - - + +
58B GLN* 3.9 39.7 - - + +
61B LEU* 3.7 25.8 - - + -
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Residues in contact with GLU 62 (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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58A GLN* 2.9 49.8 + - + +
59A TYR* 4.7 2.3 - - - -
61A LEU* 1.3 83.4 - - + +
63A ASN* 1.3 74.0 + - - +
64A GLU 5.1 0.2 - - - +
54B LYS* 4.9 0.7 - - - -
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Residues in contact with ASN 63 (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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59A TYR* 2.9 68.6 + - + +
60A LEU* 4.4 1.3 - - + +
62A GLU* 1.3 93.3 + - - +
64A GLU* 1.3 65.8 + - - +
66A THR* 3.1 16.3 + - - +
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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