Contacts of the helix formed by residues 79 - 97 (chain A) in PDB entry 3AFF
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 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.6 26.7 - - + +
27A ALA* 4.3 21.8 - - + -
30A THR* 4.1 19.5 - - - -
75A LEU 3.1 9.2 + - - +
76A ALA* 3.4 3.2 + - - -
78A VAL* 1.3 79.8 - - - +
80A GLY* 1.3 68.1 + - - +
81A SER* 4.1 4.7 - - - -
82A THR* 3.2 26.9 + - - +
83A GLY 3.0 18.0 + - - -
357A ARG* 5.9 4.7 - - - +
358A PHE* 4.7 1.1 - - - -
361A ASP* 5.9 0.2 - - - -
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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
----------------------------------------------------------
76A ALA* 3.8 6.1 + - - +
79A CYS* 1.3 73.8 - - - +
81A SER* 1.3 52.1 + - - +
83A GLY* 3.5 0.7 + - - -
84A TRP* 2.9 34.0 + - - +
187A LEU* 4.1 6.1 - - - -
248A MET* 3.6 31.9 - - - +
357A ARG* 5.8 1.2 - - - +
358A PHE* 4.4 5.5 - - - -
361A ASP* 3.6 17.6 + - - -
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 4.1 10.5 - - - -
31A GLU* 5.2 3.8 - - - +
36A LEU* 3.9 1.3 - - - -
79A CYS* 3.2 4.1 - - - -
80A GLY* 1.3 73.9 - - - +
82A THR* 1.3 59.3 + - - +
84A TRP* 3.6 0.7 - - - +
85A VAL* 3.0 35.0 + - - +
187A LEU* 3.6 11.0 - - - +
188A ARG 3.8 0.5 + - - -
189A GLY* 3.0 38.4 + - - -
190A THR* 3.5 21.8 - - - +
361A ASP* 3.9 7.2 + - - -
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Residues in contact with THR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.8 17.8 - - + +
30A THR* 4.4 4.2 + - - +
36A LEU* 3.7 22.5 - - + +
40A THR* 3.9 21.0 + - - +
44A LEU* 4.5 3.4 - - + -
75A LEU* 4.4 16.4 - - + -
79A CYS* 3.2 29.9 + - - +
81A SER* 1.3 76.4 - - - +
83A GLY* 1.3 58.5 + - - +
85A VAL* 4.0 0.9 - - - +
86A SER* 2.7 46.8 + - - +
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 4.0 5.4 - - - -
75A LEU* 3.7 23.3 - - - +
76A ALA* 3.7 15.5 - - - -
79A CYS 3.0 10.7 + - - -
82A THR* 1.3 77.6 - - - +
84A TRP* 1.3 56.0 + - - +
86A SER* 3.9 1.8 - - - -
87A SER* 3.0 30.7 + - - -
244A PRO* 3.9 8.8 - - - +
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Residues in contact with TRP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY 2.9 18.5 + - - +
81A SER 3.6 4.9 - - - +
82A THR 3.3 0.2 - - - -
83A GLY* 1.3 76.5 - - - +
85A VAL* 1.3 62.0 + - - +
87A SER* 3.7 1.9 - - - -
88A ILE* 3.2 42.2 + - + +
141A TRP* 3.8 17.1 - + - -
143A SER* 3.0 29.9 + - - -
187A LEU* 3.7 14.6 - - + -
190A THR* 3.5 19.7 - - + +
241A ILE* 3.8 38.1 - - + -
244A PRO* 3.9 15.7 - - + +
245A ILE* 4.0 8.5 - - + -
248A MET* 3.9 17.0 - - + -
365A GLY* 3.7 29.8 - - - -
368A HIS* 3.5 24.2 - + + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.7 28.7 - - + -
50A PHE* 6.4 1.1 - - + -
81A SER 3.0 23.4 + - - +
84A TRP* 1.3 70.2 - - - +
86A SER* 1.3 61.0 + - - +
88A ILE* 4.6 3.6 - - - -
89A VAL* 2.8 41.7 + - + +
143A SER* 4.6 2.7 - - - -
144A GLY* 3.6 26.7 - - - +
147A HIS* 5.7 3.8 - - + -
190A THR* 3.5 39.0 - - - +
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.8 2.0 - - - +
44A LEU* 3.2 25.5 - - - +
49A PHE* 3.2 35.4 - - - -
50A PHE* 5.0 5.8 - - - -
72A THR* 5.2 0.4 - - - -
75A LEU* 3.6 16.7 - - - +
82A THR* 2.7 25.6 + - - +
83A GLY 3.9 2.2 - - - -
85A VAL* 1.3 78.0 - - - +
87A SER* 1.3 64.7 + - - +
90A GLY 2.9 19.4 + - - -
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 3.5 8.3 - - - -
69A PHE* 4.5 1.7 - - - -
72A THR* 3.5 29.6 + - - +
83A GLY 3.0 18.7 + - - -
84A TRP 3.7 4.5 - - - -
86A SER* 1.3 77.7 - - - +
88A ILE* 1.3 56.9 + - - +
91A VAL* 3.1 31.7 + - - +
240A THR* 2.5 37.0 + - - -
244A PRO* 4.0 4.8 - - - +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TRP* 3.2 53.2 + - + +
85A VAL* 3.9 3.6 - - - +
87A SER* 1.3 74.7 - - - +
89A VAL* 1.3 66.3 + - - +
91A VAL* 3.4 2.4 - - + +
92A HIS* 3.1 52.5 + - + +
118A SER* 4.3 4.7 - - - +
143A SER* 3.8 25.6 - - - +
240A THR* 3.6 17.7 - - + +
241A ILE* 3.8 17.0 - - + -
368A HIS* 5.5 3.8 - - + -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 4.0 11.5 - - + -
85A VAL* 2.8 37.5 + - + +
88A ILE* 1.3 72.7 - - + +
90A GLY* 1.4 60.3 + - - +
92A HIS* 3.3 20.6 + - + +
93A ASN* 4.0 8.0 + - - +
115A ARG* 3.8 42.2 - - + -
116A ILE 4.0 12.6 + - - +
117A SER* 5.1 1.6 - - - -
143A SER 3.7 23.3 - - - +
144A GLY* 4.3 10.5 - - - +
147A HIS* 5.3 3.8 - - + +
148A ALA* 5.5 1.1 - - + -
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 4.3 1.3 - - - -
50A PHE* 4.2 20.0 - - - +
53A LEU* 4.2 8.1 + - - +
68A PHE* 3.8 16.5 - - - -
86A SER 2.9 22.8 + - - -
89A VAL* 1.4 74.4 - - - +
91A VAL* 1.3 59.7 + - - +
93A ASN* 3.2 24.2 + - - +
94A TRP 4.0 1.7 + - - -
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 4.2 10.5 - - + -
68A PHE* 3.6 9.3 - - + -
69A PHE* 5.0 2.5 - - + -
87A SER 3.1 16.3 + - - +
88A ILE* 3.4 13.0 - - - +
90A GLY* 1.3 72.2 - - - +
92A HIS* 1.3 76.7 + - + +
93A ASN 3.1 0.7 - - - -
94A TRP* 3.0 26.8 + - + +
95A HIS* 3.0 19.1 + - + +
120A TYR* 5.7 0.9 - - + +
236A MET* 4.2 30.1 - - + +
237A HIS* 6.1 1.8 - - - +
240A THR* 3.6 22.0 - - + +
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.1 39.1 + - + +
89A VAL* 3.3 6.5 + - - +
90A GLY 3.1 1.6 - - - -
91A VAL* 1.3 88.7 - - + +
93A ASN* 1.3 58.6 + - - +
95A HIS* 3.2 6.3 + - + +
96A LEU* 3.0 28.4 + - - +
116A ILE* 2.7 34.3 + - + +
117A SER* 3.5 5.3 - - - -
118A SER* 2.8 41.8 + - - -
120A TYR* 3.2 25.1 + + - -
152A PHE* 3.9 14.2 - + + -
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Residues in contact with ASN 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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50A PHE* 2.6 40.7 + - - +
53A LEU 3.9 5.4 - - - +
54A GLN* 4.1 20.4 - - + +
55A PRO* 3.9 2.1 - - - +
89A VAL 4.3 7.7 + - - +
90A GLY* 3.2 11.2 + - - +
91A VAL 3.1 0.6 - - - -
92A HIS* 1.3 75.1 - - - +
94A TRP* 1.3 62.1 + - - +
96A LEU 4.1 0.2 - - - -
97A ALA* 3.6 12.6 + - - +
108A TRP* 3.3 43.7 - - + -
114A THR 4.4 6.1 + - - +
115A ARG* 4.9 4.9 - - - +
116A ILE* 3.5 13.2 - - - +
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Residues in contact with TRP 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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53A LEU* 3.9 26.9 + - + +
90A GLY 4.0 1.6 + - - -
91A VAL* 3.0 27.0 + - + +
93A ASN* 1.3 77.0 - - - +
95A HIS* 1.3 81.8 + - + +
97A ALA* 3.3 16.5 - - - +
98A LEU* 3.8 31.0 + - + +
213A MET* 5.2 0.9 - - + -
228A VAL* 2.9 31.6 + - + -
229A TYR* 3.6 29.0 - + - +
231A MET* 3.4 26.7 - - + +
233A TRP* 3.8 38.4 - + + -
236A MET* 3.8 43.2 - - + +
237A HIS* 6.3 0.2 - - - -
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Residues in contact with HIS 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 VAL 3.0 12.8 + - - +
92A HIS* 3.2 7.6 + - - +
94A TRP* 1.3 88.1 - - + +
96A LEU* 1.3 58.3 + - - +
98A LEU* 3.0 22.8 + - + +
99A PHE* 3.6 20.7 - + - -
120A TYR* 2.7 34.1 + + - +
152A PHE* 3.5 14.2 - + + -
168A SER* 3.3 29.4 + - - -
208A LEU* 4.0 5.8 + - + +
213A MET* 3.7 30.8 - - + +
233A TRP* 3.6 15.0 - + + -
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Residues in contact with LEU 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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92A HIS 3.0 15.9 + - - +
94A TRP 3.3 0.4 - - - -
95A HIS* 1.3 70.7 - - - +
97A ALA* 1.3 60.6 + - - +
98A LEU 3.1 2.0 - - - -
99A PHE* 3.0 36.5 + - + +
104A GLN* 3.2 23.2 - - + +
107A VAL* 3.7 32.5 - - + -
108A TRP* 3.5 39.0 - - + -
116A ILE* 3.8 7.9 - - + -
152A PHE* 3.9 11.1 - - + -
170A LEU* 3.7 29.6 - - + -
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Residues in contact with ALA 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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55A PRO* 3.5 28.0 - - + -
93A ASN 3.6 7.2 + - - +
94A TRP 3.3 14.1 - - - +
96A LEU* 1.3 78.5 - - - +
98A LEU* 1.4 57.3 + - - +
99A PHE 3.4 0.2 - - - -
104A GLN* 4.0 4.9 - - - -
108A TRP* 4.6 1.0 - - - -
220A GLY* 3.3 13.2 - - - -
224A ASN* 2.9 29.2 + - - +
229A TYR* 3.5 23.3 - - + +
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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
------------------------------------------------------------
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