Contacts of the helix formed by residues 78 - 91 (chain A) in PDB entry 2FD5
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLY 3.7 2.0 + - - -
77A LEU* 1.3 76.4 - - - +
79A GLY* 1.3 65.3 + - - +
80A LYS* 3.6 8.0 + - - +
81A GLU* 2.8 40.1 + - - +
82A ARG* 2.9 23.5 + - - -
137A GLU* 4.5 3.6 - - - -
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Residues in contact with GLY 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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78A SER* 1.3 72.3 - - - +
80A LYS* 1.3 57.5 + - - +
82A ARG* 3.2 6.3 + - - +
83A ARG* 2.9 53.0 + - - +
135A LEU 3.9 5.8 - - - -
137A GLU* 3.2 30.4 - - - +
141A GLU* 3.9 2.8 + - - -
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Residues in contact with LYS 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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78A SER* 3.2 7.5 + - - +
79A GLY* 1.3 76.4 - - - +
81A GLU* 1.3 57.4 + - + +
83A ARG* 3.3 15.6 + - - +
84A ALA* 3.0 34.1 + - - +
141A GLU* 4.7 2.0 + - - +
179A VAL* 4.6 4.7 + - - +
180A ASN* 3.3 41.3 + - - +
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Residues in contact with GLU 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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76A GLY 4.6 0.9 - - - +
77A LEU* 3.4 25.7 - - + +
78A SER* 2.8 40.0 + - - +
80A LYS* 1.3 73.1 - - + +
82A ARG* 1.3 67.4 + - - +
84A ALA* 3.2 5.8 + - - +
85A LEU* 2.8 36.7 + - + +
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Residues in contact with ARG 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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70A LEU 5.7 0.6 + - - -
73A LEU* 3.9 22.7 - - + +
74A ASP 3.6 21.3 - - - -
75A PRO* 4.8 4.9 + - - +
77A LEU* 2.5 56.6 + - + -
78A SER 2.9 16.0 + - - +
79A GLY* 3.9 3.5 - - - +
81A GLU* 1.3 75.3 - - - +
83A ARG* 1.3 60.2 + - - +
85A LEU* 3.8 1.3 - - - +
86A ALA* 2.9 30.1 + - - +
134A SER 2.8 28.9 + - - -
135A LEU* 4.2 16.8 - - + +
136A ALA 5.5 0.6 + - - -
137A GLU* 3.2 26.6 + - - +
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Residues in contact with ARG 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 GLY 2.9 27.7 + - - +
80A LYS* 3.5 20.2 - - - +
82A ARG* 1.3 76.6 - - - +
84A ALA* 1.3 56.8 + - - +
86A ALA* 3.4 3.2 + - - +
87A ALA* 2.9 30.5 + - - +
135A LEU* 2.8 54.7 + - + +
136A ALA* 4.2 0.2 - - - +
141A GLU* 2.9 38.6 + - - +
144A VAL* 3.9 11.2 - - - +
145A ALA* 3.9 19.7 - - - +
148A ASP* 3.2 24.0 + - + +
152A MET* 4.4 3.5 - - + +
179A VAL* 3.8 4.4 - - + +
180A ASN* 2.8 39.1 + - - +
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Residues in contact with ALA 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 LYS* 3.0 21.7 + - - +
81A GLU* 3.2 7.4 + - - +
83A ARG* 1.3 75.7 - - - +
85A LEU* 1.3 60.5 + - + +
87A ALA* 3.3 3.4 + - - +
88A ALA* 2.9 29.7 + - - +
179A VAL* 4.3 11.1 - - + +
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Residues in contact with LEU 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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73A LEU* 4.3 21.8 - - + -
74A ASP* 5.8 0.7 - - + +
77A LEU* 3.7 27.1 - - + -
81A GLU* 2.8 40.5 + - + +
82A ARG* 3.8 4.5 - - - +
84A ALA* 1.3 77.6 - - + +
86A ALA* 1.3 67.5 + - - +
88A ALA* 3.2 6.6 + - - +
89A PHE* 3.0 36.4 + - + -
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Residues in contact with ALA 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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66A ARG* 5.5 0.5 + - - -
70A LEU* 3.7 28.9 - - + -
73A LEU* 4.3 5.3 - - + +
82A ARG 2.9 18.0 + - - +
83A ARG 3.7 4.5 - - - +
85A LEU* 1.3 76.3 - - - +
87A ALA* 1.3 58.2 + - - +
89A PHE* 3.3 7.9 + - - +
90A TYR* 2.9 29.8 + - - +
135A LEU* 4.4 6.1 - - + -
152A MET* 4.0 18.5 - - + +
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Residues in contact with ALA 87 (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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83A ARG 2.9 17.9 + - - +
84A ALA* 3.6 4.7 - - - +
86A ALA* 1.3 78.5 - - - +
88A ALA* 1.3 56.9 + - - +
91A LEU* 2.9 37.1 + - + +
152A MET* 4.0 17.7 - - + -
176A LYS* 3.7 12.7 - - + +
179A VAL* 3.6 31.6 - - + -
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Residues in contact with ALA 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 ALA 2.9 17.6 + - - +
85A LEU* 3.2 6.5 + - - +
87A ALA* 1.3 78.4 - - - +
89A PHE* 1.3 61.6 + - + +
91A LEU 3.9 11.4 + - - +
92A SER* 4.2 7.1 - - - -
176A LYS* 3.8 21.3 + - + +
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Residues in contact with PHE 89 (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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66A ARG* 5.0 8.9 + - - +
73A LEU* 4.0 24.9 - - + -
85A LEU* 3.0 32.2 + - + -
86A ALA* 3.7 8.3 - - - +
88A ALA* 1.3 78.0 - - + +
90A TYR* 1.3 63.3 + - - +
92A SER* 3.8 12.2 + - - -
95A HIS* 4.4 4.5 + - - +
100A VAL* 5.9 1.2 - - - +
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Residues in contact with TYR 90 (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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66A ARG* 3.5 24.2 - - - +
86A ALA 2.9 17.5 + - - +
87A ALA 3.9 2.5 - - - +
89A PHE* 1.3 76.1 - - - +
91A LEU* 1.3 60.5 + - + +
92A SER 3.1 7.1 + - - -
95A HIS* 2.7 30.1 + + - +
104A CYS* 3.1 44.8 - - + -
107A PRO* 3.3 17.7 - - - +
149A LEU* 6.3 2.0 - - + -
152A MET* 3.1 58.6 - - + -
153A ILE* 3.7 15.9 - - + +
156A LEU* 3.6 22.4 - - + +
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Residues in contact with LEU 91 (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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87A ALA* 2.9 17.9 + - + +
88A ALA 4.2 3.6 - - - -
90A TYR* 1.3 74.7 - - + +
92A SER* 1.3 58.5 + - - +
151A LEU 3.9 11.7 - - - +
152A MET* 3.5 39.7 - - + +
155A GLY* 3.9 4.0 - - - -
156A LEU* 3.6 18.4 - - + +
172A LEU* 3.9 29.1 - - + +
175A ALA* 3.9 11.9 - - + +
176A LYS* 3.2 65.5 + - + +
179A VAL* 5.0 0.7 - - + -
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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