Contacts of the helix formed by residues 86 - 101 (chain A) in PDB entry 3A3K
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 CYS 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TYR* 4.0 4.5 - - - -
18A TRP* 3.5 26.2 - - - +
60A CYS* 2.1 51.8 - - + -
85A GLY* 1.3 73.5 - - - +
87A VAL* 1.3 54.1 + - - +
88A TYR* 5.1 0.2 - - + -
89A SER* 3.7 12.9 - - - +
90A ALA* 2.7 36.8 + - - +
161A ASP* 3.4 19.7 - - - +
600A BR 3.4 4.0 - - - +
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Residues in contact with VAL 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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85A GLY 3.6 1.8 + - - -
86A CYS* 1.3 70.1 - - - +
88A TYR* 1.3 62.9 + - + +
90A ALA* 3.2 6.0 + - - +
91A ALA* 2.9 35.8 + - + +
109A ALA* 4.6 3.4 - - - +
110A PRO* 4.1 16.8 - - + -
111A ALA* 3.6 38.4 - - + +
114A ILE* 5.0 4.8 - - + +
161A ASP* 3.0 19.0 + - - +
166A PHE* 3.6 42.8 - - + -
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Residues in contact with TYR 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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60A CYS 5.6 4.0 - - - +
61A SER 5.3 0.7 - - - -
62A ASP* 3.4 32.3 - - + +
86A CYS* 5.1 0.7 - - + -
87A VAL* 1.3 82.7 - - + +
89A SER* 1.3 56.4 + - - +
91A ALA* 4.5 4.9 - - + +
92A PRO* 3.1 20.6 - - - +
160A ASP 3.0 28.7 - - - -
161A ASP* 3.2 27.0 + - - +
162A ARG* 3.4 32.1 + - - -
166A PHE* 3.7 24.6 - + - -
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Residues in contact with SER 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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53A SER* 3.9 1.6 - - - -
60A CYS* 3.8 10.0 - - - +
61A SER 2.9 34.3 + - - -
65A ALA* 3.6 12.8 - - - +
84A PRO* 3.6 21.5 - - - -
86A CYS* 3.2 12.4 + - - +
88A TYR* 1.3 76.2 - - - +
90A ALA* 1.3 66.5 + - - +
92A PRO* 3.3 11.2 - - - +
93A VAL* 3.3 20.1 - - - +
600A BR 4.2 2.9 - - - -
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Residues in contact with ALA 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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84A PRO* 3.9 24.4 - - + +
86A CYS 2.7 20.9 + - - +
87A VAL 3.8 3.4 - - - +
89A SER* 1.3 74.7 - - - +
91A ALA* 1.3 64.1 + - - +
94A GLY* 2.9 24.8 + - - -
104A LEU* 5.3 3.6 - - + +
106A THR* 5.8 0.7 - - + -
109A ALA* 3.7 28.7 - - + -
114A ILE* 4.5 6.9 - - + +
120A TYR* 4.3 1.7 - - - -
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Residues in contact with ALA 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 VAL* 2.9 19.9 + - + +
88A TYR* 4.5 5.2 - - + +
90A ALA* 1.3 77.0 - - - +
92A PRO* 1.4 70.9 - - + +
95A ARG* 3.5 8.2 + - - +
114A ILE* 4.1 10.9 - - + +
120A TYR* 3.1 36.8 + - - +
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Residues in contact with PRO 92 (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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62A ASP* 3.6 21.8 - - + +
66A PRO* 4.0 19.3 - - + -
88A TYR 3.1 24.2 - - - +
89A SER 3.3 10.8 - - - +
91A ALA* 1.4 89.6 - - + +
93A VAL* 1.3 62.5 + - - +
95A ARG* 3.4 7.6 + - + +
96A PHE* 3.3 29.0 + - + -
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Residues in contact with VAL 93 (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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8A VAL* 4.9 2.2 - - + -
65A ALA* 3.7 9.6 - - + +
66A PRO* 3.6 30.1 - - + -
69A ALA* 4.0 18.8 - - + -
81A PHE* 4.7 5.8 - - + -
84A PRO* 3.8 23.1 - - + -
89A SER 3.3 17.2 + - - +
90A ALA 3.3 2.2 + - - +
92A PRO* 1.3 76.9 - - - +
94A GLY* 1.3 58.7 + - - +
96A PHE* 3.1 9.6 + - - +
97A THR* 2.9 31.5 + - + +
104A LEU* 3.7 19.7 - - + -
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Residues in contact with GLY 94 (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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90A ALA 2.9 16.0 + - - -
93A VAL* 1.3 75.1 - - - +
95A ARG* 1.3 58.4 + - - +
97A THR* 3.1 19.3 + - - -
98A ALA* 3.1 18.7 + - - +
104A LEU* 4.1 10.2 - - - +
120A TYR* 3.7 22.8 - - - -
121A ALA 4.8 0.2 - - - +
123A THR* 4.5 5.6 + - - -
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Residues in contact with ARG 95 (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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91A ALA 3.5 14.5 + - - +
92A PRO* 3.4 10.2 + - + +
93A VAL 3.3 0.4 - - - -
94A GLY* 1.3 74.1 - - - +
96A PHE* 1.3 65.3 + - + +
98A ALA* 3.6 4.6 + - - +
99A HIS* 3.2 22.3 + - - +
119A GLU* 3.6 47.9 + - - +
120A TYR* 3.9 20.8 + - - +
503A SO4 2.8 43.8 + - - -
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Residues in contact with PHE 96 (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 PRO* 4.1 25.1 - - + -
69A ALA* 5.7 1.8 - - + -
70A VAL* 4.0 20.9 - - + -
92A PRO* 3.3 22.7 + - + -
93A VAL* 3.1 11.0 + - + +
95A ARG* 1.3 75.7 - - + +
97A THR* 1.3 60.5 + - - +
99A HIS* 3.0 13.5 + + + +
100A TRP* 2.9 71.1 + + + -
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Residues in contact with THR 97 (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 PHE* 3.8 35.0 - - + -
93A VAL* 2.9 21.1 + - + +
94A GLY* 3.1 19.6 + - - -
96A PHE* 1.3 74.2 - - - +
98A ALA* 1.3 56.2 + - - +
100A TRP* 3.3 13.0 + - + -
101A ARG 2.9 22.3 + - - -
102A VAL* 3.0 30.3 + - - +
104A LEU* 3.7 24.9 - - + +
121A ALA 4.9 2.1 + - - -
123A THR* 4.7 1.7 + - - -
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Residues in contact with ALA 98 (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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94A GLY 3.1 19.3 + - - +
95A ARG* 3.6 6.1 - - - +
96A PHE 3.2 0.2 - - - -
97A THR* 1.3 78.9 + - - +
99A HIS* 1.3 61.2 + - - +
101A ARG* 3.1 20.2 + - - +
119A GLU 3.3 23.8 - - - +
121A ALA* 3.8 31.1 - - + +
122A LEU* 5.7 0.2 - - - +
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Residues in contact with HIS 99 (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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95A ARG 3.2 11.1 + - - +
96A PHE* 3.0 15.1 + + - +
98A ALA* 1.3 78.5 - - - +
100A TRP* 1.3 79.3 + + - +
101A ARG* 3.5 6.6 + - - +
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Residues in contact with TRP 100 (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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69A ALA* 3.8 13.9 - - + -
70A VAL* 3.9 18.6 - - + -
73A LYS* 3.7 61.3 - - + +
81A PHE* 3.8 22.4 - + - -
96A PHE* 2.9 56.1 + + + +
97A THR* 3.7 16.6 - - + +
98A ALA 3.2 0.4 - - - -
99A HIS* 1.3 93.6 - + - +
101A ARG* 1.3 69.2 + - - +
102A VAL* 3.3 11.5 + - + +
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Residues in contact with ARG 101 (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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97A THR 2.9 5.8 + - - -
98A ALA 3.1 14.6 + - - +
99A HIS 4.1 6.7 - - - +
100A TRP* 1.3 80.8 - - - +
102A VAL* 1.3 59.0 - - - +
103A PRO* 4.0 3.1 - - - +
122A LEU* 3.3 25.5 - - + +
343A THR 4.9 3.8 - - - +
345A GLY* 4.3 7.6 + - - -
346A GLU* 5.1 14.1 - - - +
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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