Contacts of the helix formed by residues 85 - 102 (chain b) in PDB entry 5A0Q
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 85 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49b THR* 4.2 18.9 - - + -
84b SER* 1.3 84.2 - - - +
86b ARG* 1.3 64.6 + - + +
88b ILE* 3.4 8.3 + - + +
89b HIS* 3.0 29.8 + - - +
112b ILE* 4.5 10.4 - - + +
114b GLY* 3.5 39.7 - - - +
116b ALA* 3.6 21.1 - - + -
121b PHE* 3.5 24.5 - - + -
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Residues in contact with ARG 86 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99T PHE 4.6 0.7 - - - -
100T ASP* 5.5 12.8 - - + +
84b SER* 3.2 7.5 - - - +
85b PRO* 1.3 83.8 - - - +
87b ALA* 1.3 58.0 + - - +
89b HIS* 3.8 3.3 - - + +
90b SER* 2.9 29.4 + - - -
116b ALA* 5.3 4.8 - - - +
119b GLU* 3.2 33.5 + - - +
121b PHE* 3.1 49.9 - - + +
133b GLU* 5.3 1.4 - - - +
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Residues in contact with ALA 87 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99T PHE* 3.3 39.1 + - + +
101T ARG* 4.6 10.8 - - + +
84b SER* 3.2 25.5 + - - +
85b PRO 3.2 0.2 - - - -
86b ARG* 1.3 79.7 - - - +
88b ILE* 1.3 61.5 + - + +
90b SER* 3.3 1.7 + - - -
91b TRP* 2.9 29.8 + - - +
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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
----------------------------------------------------------
99T PHE* 6.1 1.1 - - + -
45b VAL* 4.7 8.1 - - + -
46b ASN* 5.1 1.6 - - - +
49b THR* 5.2 4.3 - - - +
51b LEU* 4.0 15.3 - - + -
67b LEU* 3.7 34.1 - - + +
70b MET* 5.5 6.1 - - + -
71b VAL* 3.8 29.4 - - + -
84b SER 3.2 16.5 + - - +
85b PRO* 3.4 9.6 + - + +
87b ALA* 1.3 77.4 - - + +
89b HIS* 1.3 57.2 + - - +
91b TRP* 3.5 5.7 + - + +
92b LEU* 2.9 26.9 + - + +
112b ILE* 4.1 8.7 - - + -
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Residues in contact with HIS 89 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85b PRO 3.0 17.6 + - - +
86b ARG* 3.8 2.2 - - + +
88b ILE* 1.3 73.4 - - - +
90b SER* 1.3 67.1 + - - +
92b LEU* 3.5 3.2 - - - +
93b THR* 2.8 36.8 + - - -
112b ILE* 3.3 25.1 - - + +
121b PHE* 3.7 22.9 - + + -
123b GLY* 3.5 6.0 - - - -
124b TYR 3.0 32.8 - - - -
125b VAL* 3.0 20.1 - - + +
131b ALA* 3.1 23.5 - - + +
132b TYR* 3.8 11.5 + - - -
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Residues in contact with SER 90 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98T VAL 3.5 2.4 + - - -
99T PHE 3.3 14.8 - - - -
100T ASP* 1.7 42.0 + - - +
86b ARG 2.9 18.7 + - - -
87b ALA 3.4 6.3 - - - -
89b HIS* 1.3 83.6 - - - +
91b TRP* 1.3 64.3 + - - +
93b THR* 3.2 1.4 + - - -
94b ARG* 2.9 35.3 + - - +
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Residues in contact with TRP 91 (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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97T PHE* 5.8 0.7 - + - -
98T VAL* 3.1 38.7 + - + +
99T PHE* 4.1 12.6 - + + -
66b VAL* 5.6 4.6 - - + +
67b LEU* 6.3 0.2 - - - -
70b MET* 3.2 43.1 - - + +
87b ALA 2.9 15.1 + - - +
88b ILE* 4.0 6.7 - - + +
90b SER* 1.3 76.2 - - - +
92b LEU* 1.3 57.0 + - + +
94b ARG* 2.4 81.8 + - + +
95b ALA* 2.8 22.6 + - + +
98b SER* 5.3 4.7 - - - -
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Residues in contact with LEU 92 (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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51b LEU* 3.3 25.6 - - + -
63b LEU* 4.0 17.9 - - + -
67b LEU* 4.0 24.0 - - + -
88b ILE 2.9 18.2 + - - +
89b HIS* 3.2 6.3 + - - +
91b TRP* 1.3 76.7 - - + +
93b THR* 1.3 57.0 + - - +
95b ALA* 3.2 6.8 + - + +
96b MET* 3.0 37.1 + - - +
110b MET* 3.8 29.2 - - + -
112b ILE* 4.0 9.9 - - + -
125b VAL* 3.9 22.4 - - + -
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Residues in contact with THR 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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62a LEU* 4.8 8.7 - - + -
63a THR* 5.2 5.8 - - - +
66a LYS* 5.9 0.7 - - - -
89b HIS* 2.8 20.6 + - - -
90b SER* 3.4 10.5 - - - -
92b LEU* 1.3 74.1 - - - +
94b ARG* 1.3 71.7 + - - +
96b MET* 4.1 0.4 - - - +
97b TYR* 2.9 36.7 + - + +
125b VAL* 3.7 13.3 - - - +
129b GLY* 3.4 23.3 - - - +
131b ALA* 3.2 26.4 - - + +
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Residues in contact with ARG 94 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97T PHE* 3.0 46.8 + - - -
98T VAL* 3.7 4.2 + - - +
100T ASP* 2.3 33.1 + - - -
62a LEU* 5.9 0.2 - - - +
63a THR* 5.5 3.8 + - - -
66a LYS* 3.3 33.5 - - - +
90b SER* 2.9 26.8 + - - +
91b TRP* 2.4 60.9 + - + -
93b THR* 1.3 95.6 - - - +
95b ALA* 1.3 53.5 + - - -
97b TYR* 3.8 4.9 - - - +
98b SER* 3.0 34.3 + - - +
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Residues in contact with ALA 95 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62b TYR* 6.0 1.3 - - - +
63b LEU* 4.4 26.0 - - + -
66b VAL* 6.3 0.9 - - + -
91b TRP* 2.8 24.2 + - + +
92b LEU* 3.2 13.0 + - + +
94b ARG* 1.3 73.4 - - - +
96b MET* 1.4 63.2 + - - +
98b SER* 3.3 5.2 + - - -
99b ARG* 3.2 29.1 + - - +
106b LEU* 4.5 2.7 - - - -
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Residues in contact with MET 96 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63b LEU* 3.5 29.8 - - - -
92b LEU* 3.0 21.4 + - - +
93b THR 4.1 1.3 - - - +
95b ALA* 1.4 74.9 - - - +
97b TYR* 1.3 60.6 + - - +
99b ARG* 3.8 2.4 + - - +
100b ARG* 3.3 17.8 + - - +
105b PRO* 5.3 0.5 - - - +
106b LEU* 3.7 30.5 - - + +
108b ASN* 3.1 35.0 - - + +
110b MET* 4.0 9.0 - - + -
125b VAL* 3.4 22.9 - - + +
126b ASP 3.7 7.2 - - - +
127b MET* 3.6 27.4 - - - +
129b GLY* 4.0 7.9 - - - -
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Residues in contact with TYR 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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59a GLY 3.5 14.1 - - - -
60a ASP* 3.2 22.7 + - - -
63a THR* 3.4 41.7 - - + +
99a ARG* 4.0 0.7 - - - -
104a TYR* 2.7 38.8 - + - -
93b THR* 2.9 21.9 + - + +
94b ARG* 3.8 5.8 - - - +
96b MET* 1.3 76.4 - - - +
98b SER* 1.3 66.2 + - - +
100b ARG* 3.1 24.3 + - - +
101b SER* 3.0 40.9 + - - -
128b LEU 4.8 9.0 - - - -
129b GLY* 4.3 10.0 - - - -
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Residues in contact with SER 98 (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 TRP* 5.3 4.3 - - - -
94b ARG* 3.0 24.2 + - - +
95b ALA* 3.3 6.2 + - - -
97b TYR* 1.3 80.3 - - - +
99b ARG* 1.3 62.2 + - - +
101b SER* 3.3 20.9 + - - -
102b LYS* 3.0 21.5 + - - +
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Residues in contact with ARG 99 (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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88V TYR* 5.2 6.7 + - - -
91V ARG* 4.5 15.2 - - - +
59b ASP* 4.0 13.7 + - - -
62b TYR* 3.8 36.9 + - - +
95b ALA 3.2 8.1 + - - +
96b MET 4.1 0.7 - - - +
98b SER* 1.3 75.9 - - - +
100b ARG* 1.3 59.9 + - - +
101b SER 3.5 0.2 + - - -
102b LYS* 3.6 22.2 + - - +
103b MET 3.6 1.2 + - - -
104b ASN* 2.8 78.0 + - - +
105b PRO* 3.1 19.5 + - + -
106b LEU* 3.5 27.3 - - + +
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Residues in contact with ARG 100 (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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57a PHE* 3.9 14.8 - - - -
60a ASP* 3.1 31.1 + - - -
99a ARG* 3.1 33.0 - - - +
102a PHE* 3.4 28.8 - - + -
103a PRO 4.5 3.0 + - - -
96b MET 3.3 14.8 + - - +
97b TYR* 3.1 26.9 + - - +
99b ARG* 1.3 76.0 - - - +
101b SER* 1.3 58.5 + - - +
103b MET* 2.9 21.7 + - - +
105b PRO* 4.1 13.6 - - + +
128b LEU* 3.4 44.0 - - + +
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Residues in contact with SER 101 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99a ARG* 4.4 12.4 + - - +
102a PHE* 3.3 29.7 - - - -
97b TYR* 3.0 32.6 + - - -
98b SER* 3.3 12.8 + - - -
100b ARG* 1.3 77.4 + - - +
102b LYS* 1.4 60.1 + - - +
103b MET* 3.2 4.0 - - - +
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Residues in contact with LYS 102 (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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98b SER* 3.0 32.1 + - - +
99b ARG* 3.6 31.3 + - - +
100b ARG 3.2 0.4 - - - -
101b SER* 1.4 75.4 - - - +
103b MET* 1.3 77.3 + - - +
104b ASN* 4.2 19.8 - - + +
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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