Contacts of the helix formed by residues 79 - 97 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.8 23.3 - - + +
27B ALA* 4.1 23.1 - - + -
30B THR* 4.1 20.4 - - - -
75B LEU 3.1 8.0 + - - +
76B ALA* 3.4 3.7 + - - -
78B VAL* 1.3 78.3 - - - +
80B GLY* 1.3 67.8 + - - +
81B SER* 3.2 6.3 - - - -
82B THR* 3.1 24.9 + - - -
83B GLY 3.1 18.0 + - - -
357B ARG* 4.6 7.6 - - - +
358B PHE* 4.7 0.2 - - - -
361B ASP* 5.8 0.2 - - - -
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ALA* 3.5 4.6 + - - -
79B CYS* 1.3 71.9 - - - +
81B SER* 1.3 62.6 + - - +
83B GLY* 3.5 1.0 + - - -
84B TRP* 3.0 24.6 + - - +
187B LEU* 4.0 2.9 - - - -
248B MET* 3.5 36.3 - - - +
357B ARG* 5.0 1.8 - - - +
358B PHE* 4.4 6.9 - - - -
361B ASP* 3.6 17.0 + - - -
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 4.2 4.3 - - - -
31B GLU* 5.7 2.4 - - - +
36B LEU* 4.0 2.0 - - - -
79B CYS* 3.2 11.7 - - - -
80B GLY* 1.3 75.2 - - - +
82B THR* 1.3 57.7 + - - +
84B TRP* 3.4 1.2 + - - +
85B VAL* 3.1 34.5 + - - +
187B LEU* 3.5 18.9 - - - -
188B ARG 3.8 0.2 + - - -
189B GLY* 3.2 43.4 + - - -
190B THR* 3.7 8.2 - - - +
361B ASP* 3.8 6.9 + - - -
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Residues in contact with THR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 4.0 15.9 - - + +
30B THR* 4.4 4.7 + - - +
36B LEU* 3.4 21.3 - - + +
40B THR* 3.9 26.3 + - + +
44B LEU* 4.6 1.1 - - + -
75B LEU* 4.1 17.9 - - + -
79B CYS* 3.1 28.3 + - - +
81B SER* 1.3 77.1 - - - +
83B GLY* 1.3 58.3 + - - +
85B VAL* 4.2 0.7 - - - +
86B SER* 2.7 45.3 + - - +
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.9 5.3 - - - -
75B LEU* 3.6 22.4 - - - +
76B ALA* 3.7 14.8 - - - -
79B CYS 3.1 10.5 + - - -
82B THR* 1.3 78.8 - - - +
84B TRP* 1.3 56.2 + - - +
86B SER* 4.0 1.7 - - - -
87B SER* 3.1 30.8 + - - -
244B PRO* 3.8 9.7 - - - +
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Residues in contact with TRP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY 3.0 18.9 + - - +
81B SER 3.5 4.7 - - - +
82B THR 3.2 0.2 - - - -
83B GLY* 1.3 75.9 - - - +
85B VAL* 1.3 65.7 + - - +
87B SER* 3.8 1.6 - - - -
88B ILE* 3.1 43.2 + - + +
141B TRP* 3.6 17.7 - + - -
143B SER* 3.1 26.1 + - - -
187B LEU* 3.8 17.5 - - + -
190B THR* 3.5 22.0 - - + -
241B ILE* 3.6 42.6 - - + -
244B PRO* 4.0 16.2 - - + +
245B ILE* 4.1 4.0 - - + -
248B MET* 4.1 12.6 - - + -
365B GLY* 3.7 30.7 - - - -
368B HIS* 3.5 26.2 - + + -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.7 32.5 - - + -
41B VAL* 5.9 0.7 - - + -
50B PHE* 6.3 2.5 - - + -
81B SER 3.1 17.0 + - - +
84B TRP* 1.3 78.0 - - - +
86B SER* 1.3 59.9 + - - +
88B ILE* 3.4 3.6 + - - -
89B VAL* 2.9 37.3 + - + +
143B SER* 4.4 3.6 - - - -
144B GLY* 3.9 24.9 - - - +
147B HIS* 5.4 4.0 - - + -
190B THR* 3.7 38.4 - - - +
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.6 2.6 - - - +
44B LEU* 3.4 26.5 - - - +
49B PHE* 3.0 35.4 - - - -
50B PHE* 4.8 5.4 - - - -
72B THR* 5.4 0.4 - - - -
75B LEU* 3.6 16.0 - - - +
82B THR* 2.7 23.6 + - - +
83B GLY 4.0 1.8 - - - -
85B VAL* 1.3 75.2 - - - +
87B SER* 1.3 61.0 + - - +
90B GLY 2.8 24.9 + - - +
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.6 7.0 - - - -
69B PHE* 4.4 2.3 - - - -
72B THR* 3.4 33.2 + - - +
83B GLY 3.1 19.4 + - - -
84B TRP 3.8 2.9 - - - -
85B VAL 3.5 0.2 - - - -
86B SER* 1.3 76.6 - - - +
88B ILE* 1.3 57.4 + - - +
91B VAL* 3.0 33.4 + - - +
240B THR* 2.8 34.6 + - - +
244B PRO* 4.0 3.7 - - - +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B TRP* 3.1 49.0 + - + +
85B VAL* 3.9 4.0 - - - +
87B SER* 1.3 71.7 - - - +
89B VAL* 1.3 66.1 + - - +
91B VAL* 3.3 1.6 - - - +
92B HIS* 3.1 52.1 + - + +
118B SER* 4.4 4.7 - - - +
143B SER* 3.8 25.1 - - - +
240B THR* 3.6 22.9 - - + +
241B ILE* 3.6 19.7 - - + -
368B HIS* 5.6 2.9 - - + -
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.8 21.6 - - + -
85B VAL* 2.9 32.4 + - + +
88B ILE* 1.3 76.0 - - + +
90B GLY* 1.3 64.3 + - - +
92B HIS* 3.4 20.7 + - + +
93B ASN* 3.9 9.0 + - - +
115B ARG* 3.9 28.9 - - + -
116B ILE 4.0 11.7 + - - +
117B SER* 5.0 3.6 - - - -
143B SER 3.7 22.7 - - - +
144B GLY* 4.4 9.2 - - - +
147B HIS* 5.4 4.0 - - + +
148B ALA* 5.5 1.6 - - + -
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE* 4.3 1.1 - - - -
50B PHE* 4.1 19.8 - - - +
53B LEU* 4.4 5.9 + - - +
68B PHE* 3.8 18.3 - - - -
86B SER 2.8 20.3 + - - -
89B VAL* 1.3 80.6 - - - +
91B VAL* 1.3 58.7 + - - +
93B ASN* 3.2 22.8 + - - +
94B TRP 4.0 1.4 + - - -
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.1 20.0 - - + -
68B PHE* 3.6 8.4 - - + -
69B PHE* 5.0 2.0 - - + -
87B SER 3.0 18.1 + - - +
88B ILE 3.3 11.9 - - - +
90B GLY* 1.3 71.6 - - - +
92B HIS* 1.3 73.4 + - + +
93B ASN 3.1 2.7 - - - -
94B TRP* 3.0 26.4 + - + +
95B HIS* 3.2 10.8 + - + +
120B TYR* 5.6 1.3 - - + +
236B MET* 4.0 24.7 - - + +
240B THR* 3.6 30.5 - - + +
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Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 3.1 39.7 + - + +
89B VAL* 3.6 7.9 - - + +
90B GLY 3.2 1.0 - - - -
91B VAL* 1.3 86.5 - - + +
93B ASN* 1.3 58.6 + - - +
95B HIS* 3.6 6.4 - - + +
96B LEU* 2.9 30.8 + - - +
116B ILE* 2.6 33.7 + - + +
117B SER* 3.5 4.4 - - - -
118B SER* 2.8 42.6 + - - -
120B TYR* 3.2 25.0 + + - -
143B SER 5.5 0.2 - - - -
152B PHE* 3.9 14.1 - + + -
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Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PHE* 2.7 40.3 + - - +
53B LEU 3.9 6.0 - - - +
54B GLN* 4.1 23.1 + - + +
55B PRO* 4.1 1.4 - - - +
89B VAL 4.2 8.0 + - - +
90B GLY 3.2 13.1 + - - +
91B VAL 3.1 0.6 - - - -
92B HIS* 1.3 74.9 - - - +
94B TRP* 1.3 62.8 + - - +
97B ALA* 3.4 18.7 + - - +
108B TRP* 3.3 36.9 + - + -
114B THR 4.4 6.7 + - - +
115B ARG* 5.0 2.8 - - - +
116B ILE* 3.4 15.9 + - - +
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Residues in contact with TRP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.9 32.5 + - + +
90B GLY 4.0 1.4 + - - -
91B VAL* 3.0 19.3 + - + +
93B ASN* 1.3 77.2 - - - +
95B HIS* 1.3 81.5 + - + +
97B ALA* 3.2 17.3 + - - +
98B LEU* 3.8 22.6 - - + +
213B MET* 3.8 20.0 - - + -
228B VAL* 2.8 36.9 + - + +
229B TYR* 3.6 31.0 - + - +
231B MET* 3.3 26.7 - - + +
233B TRP* 3.8 29.8 - + - -
236B MET* 3.9 36.5 - - + +
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Residues in contact with HIS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B VAL* 3.2 10.9 + - + +
92B HIS* 3.3 8.3 + - + +
94B TRP* 1.3 87.8 - - + +
96B LEU* 1.3 58.9 + - - +
98B LEU* 3.1 22.2 + - + +
99B PHE* 3.6 18.8 - + - -
120B TYR* 2.6 48.8 + + - +
152B PHE* 3.6 12.1 - + + -
168B SER* 3.3 21.2 + - - -
208B LEU* 4.1 5.4 - - + +
210B TYR* 5.5 0.6 - - - -
213B MET* 3.9 24.2 - - - -
233B TRP* 3.7 17.8 - + + -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B HIS 2.9 17.1 + - - +
95B HIS* 1.3 72.8 - - - +
97B ALA* 1.3 59.7 + - - +
98B LEU 3.0 6.3 + - - -
99B PHE* 3.2 31.5 + - + +
103B ALA* 4.7 4.9 - - + +
104B GLN* 3.3 18.8 - - + +
107B VAL* 3.7 28.5 - - + -
108B TRP* 3.6 41.1 - - + -
116B ILE* 3.8 10.3 - - + -
152B PHE* 3.9 12.3 - - + -
170B LEU* 3.9 28.0 - - + -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PRO* 3.3 31.2 - - + -
93B ASN 3.4 6.1 + - - +
94B TRP 3.2 14.0 + - - +
96B LEU* 1.3 76.7 - - - +
98B LEU* 1.3 58.2 + - - +
99B PHE 3.5 0.2 - - - -
104B GLN* 3.8 4.7 - - - -
108B TRP* 4.5 1.0 - - - -
220B GLY* 3.1 14.9 - - - -
224B ASN* 2.8 28.3 + - - +
229B TYR* 3.5 22.6 - - + -
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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
------------------------------------------------------------
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