Contacts of the helix formed by residues 77 - 88 (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 PRO 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LEU* 6.2 0.7 - - + -
75A GLY 3.3 10.5 - - - +
76A ILE* 1.3 85.7 - - + +
78A GLU* 1.3 57.3 + - - +
80A GLY* 2.9 18.3 + - - -
81A ARG* 3.0 37.4 + - - +
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ILE* 3.3 11.5 - - + +
77A PRO* 1.3 78.6 - - - +
79A PHE* 1.3 57.7 + - - +
81A ARG* 3.3 31.3 + - - +
82A CYS* 2.9 38.3 + - - +
307A ALA* 4.2 14.8 - - + -
311A SER* 3.8 26.6 - - - +
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Residues in contact with PHE 79 (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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76A ILE* 3.0 28.0 + - + +
78A GLU* 1.3 77.8 - - - +
80A GLY* 1.4 62.1 + - - +
82A CYS* 3.4 4.7 + - + +
83A THR* 2.9 43.1 + - - -
102A THR* 5.3 0.4 - - + -
104A GLN* 3.8 30.3 - - + -
256A TYR* 3.1 41.5 - + - -
267A VAL* 3.9 14.6 - - + -
268A GLY 3.8 16.6 - - - -
269A ALA* 3.9 9.9 - - + -
303A ALA* 3.7 24.5 - - + +
306A VAL* 3.8 14.8 - - + -
307A ALA* 4.1 10.7 - - + +
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Residues in contact with GLY 80 (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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76A ILE 3.1 4.5 + - - -
77A PRO* 2.9 8.2 + - - -
79A PHE* 1.4 83.2 - - - +
81A ARG* 1.3 64.7 + - - +
83A THR* 3.2 2.9 + - - -
84A GLN* 2.9 30.9 + - - +
102A THR* 4.1 23.8 - - - -
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Residues in contact with ARG 81 (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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77A PRO* 3.0 35.3 + - - +
78A GLU* 3.3 37.7 + - - +
80A GLY* 1.3 75.6 - - - +
82A CYS* 1.3 63.0 + - - +
84A GLN* 3.3 9.8 + - - +
85A GLU* 3.1 33.2 + - + +
95A ILE* 6.5 1.3 - - + -
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Residues in contact with CYS 82 (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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78A GLU* 2.9 39.4 + - - +
79A PHE* 3.8 5.8 - - - +
81A ARG* 1.3 74.9 - - - +
83A THR* 1.3 64.5 + - - +
85A GLU* 3.3 9.1 + - - +
86A LEU* 3.1 24.0 + - - +
256A TYR* 4.6 1.1 - - - -
306A VAL* 6.1 1.1 - - + -
307A ALA* 4.8 5.2 - - - -
310A LEU* 3.9 47.3 - - + +
311A SER* 4.4 3.1 - - - -
316A ARG* 6.3 0.2 - - - -
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Residues in contact with THR 83 (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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79A PHE* 2.9 30.7 + - - -
80A GLY 3.7 4.3 - - - -
82A CYS* 1.3 73.2 - - - +
84A GLN* 1.4 66.7 + - - +
86A LEU* 3.2 4.2 + - - +
87A LEU* 2.9 45.5 + - + +
102A THR* 4.5 5.6 - - - -
254A SER* 4.1 15.0 - - - +
256A TYR* 2.4 41.5 + - + +
269A ALA* 4.1 12.6 - - + -
271A THR* 4.5 3.4 - - - +
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Residues in contact with GLN 84 (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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80A GLY 2.9 17.6 + - - +
81A ARG* 3.3 8.6 + - - +
83A THR* 1.4 73.8 - - - +
85A GLU* 1.3 59.7 + - - +
87A LEU* 3.2 3.0 + - - +
88A PHE* 2.8 52.9 + - + +
95A ILE* 4.0 29.9 - - + +
98A LYS* 4.0 9.7 + - - +
100A ALA* 2.6 44.3 + - + +
101A ARG* 3.6 0.5 + - - -
102A THR* 3.2 30.1 + - - +
271A THR* 4.5 0.9 - - + -
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Residues in contact with GLU 85 (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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81A ARG* 3.1 20.2 + - + +
82A CYS* 3.7 11.2 - - - +
83A THR 3.1 0.2 - - - -
84A GLN* 1.3 77.4 - - - +
86A LEU* 1.3 58.1 + - - +
89A GLY* 3.0 29.9 + - - +
90A LYS* 3.9 45.2 + - + +
95A ILE* 4.2 19.0 - - + +
234A GLU* 4.4 3.3 - - - +
241A ARG* 4.2 0.7 + - - -
316A ARG* 5.8 1.9 + - - -
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Residues in contact with LEU 86 (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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82A CYS 3.1 10.2 + - - +
83A THR* 3.5 9.0 - - - +
85A GLU* 1.3 78.4 - - - +
87A LEU* 1.4 58.8 + - + +
226A GLN* 2.9 43.9 - - - +
233A LEU* 4.3 20.4 - - + -
234A GLU* 4.2 7.0 - - - +
241A ARG* 3.1 15.9 + - - -
256A TYR* 3.9 22.9 - - + +
259A ASN* 5.6 2.2 - - - +
260A PHE* 5.4 0.2 - - + -
310A LEU* 3.7 27.6 - - + -
316A ARG* 4.0 26.2 - - - +
319A TRP* 4.7 10.5 - - + -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A THR* 2.9 35.8 + - + +
84A GLN* 3.4 4.3 - - - +
86A LEU* 1.4 77.0 - - + +
88A PHE* 1.3 81.2 + - + +
223A PHE* 4.4 12.1 - - + -
226A GLN* 4.0 18.8 - - - +
237A ALA* 3.5 5.5 - - - +
240A LEU* 4.0 19.2 - - + +
241A ARG* 2.8 27.4 + - - -
252A VAL* 4.6 10.1 - - + -
254A SER* 4.4 11.9 - - - +
256A TYR* 5.7 0.2 - - - +
271A THR* 3.5 31.2 - - + +
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Residues in contact with PHE 88 (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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84A GLN* 2.8 28.0 + - + +
87A LEU* 1.3 88.7 - - + +
89A GLY* 1.3 58.1 + - - +
92A SER* 3.8 26.6 - - - +
94A LEU* 4.1 27.8 - - + -
95A ILE* 4.6 5.4 - - + -
100A ALA* 4.1 8.1 - - + -
240A LEU* 4.0 30.5 - - + -
241A ARG* 3.4 23.8 + - + +
244A ALA* 4.3 13.9 - - + -
250A LEU* 4.7 2.7 - - + -
252A VAL* 4.5 5.6 - - + -
271A THR* 3.7 31.4 - - + -
273A VAL* 4.0 12.1 - - + -
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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