Contacts of the helix formed by residues 82 - 97 (chain A) in PDB entry 1B3U
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A THR* 3.9 4.4 - - + -
81A GLY* 1.3 82.4 - - - +
83A GLU* 1.3 63.5 + - + +
84A TYR 3.2 1.0 + - - -
85A VAL* 3.2 30.6 - - + +
117A GLU* 3.9 31.7 - - - +
119A SER 5.7 0.5 + - - -
122A ASP* 4.1 8.1 - - - +
322B MET* 6.4 2.7 - - + -
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Residues in contact with GLU 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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80A GLY 4.4 5.3 - - - +
81A GLY 2.9 1.0 + - - -
82A PRO* 1.3 79.6 - - + +
84A TYR* 1.3 93.2 + - + +
86A HIS* 3.7 15.2 + - - -
122A ASP* 4.7 5.7 - - - +
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Residues in contact with TYR 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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47A ARG* 2.8 48.6 + - - -
79A VAL* 3.7 22.0 - - - +
80A GLY* 3.7 21.8 - - - -
81A GLY 2.8 7.1 + - - +
83A GLU* 1.3 111.3 + - + +
85A VAL* 1.3 64.6 + - - +
86A HIS* 3.2 10.5 - + - -
87A CYS* 3.0 31.5 + - - +
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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
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76A THR* 3.2 39.0 - - + +
79A VAL* 4.8 1.8 - - - -
81A GLY 3.5 1.4 + - - -
82A PRO* 3.2 21.3 - - + +
84A TYR* 1.3 76.7 - - - +
86A HIS* 1.3 59.1 + - - +
87A CYS 2.8 6.8 + - - -
88A LEU* 2.8 32.8 + - + +
89A LEU 4.2 0.3 + - - -
114A ILE* 4.8 3.9 - - + +
117A GLU* 3.6 22.7 - - + +
118A HIS* 3.5 38.3 + - + +
122A ASP* 4.9 5.4 - - - +
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Residues in contact with HIS 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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83A GLU 3.7 20.3 + - - -
84A TYR* 3.9 14.1 - + - -
85A VAL* 1.3 80.6 + - + +
87A CYS* 1.3 72.0 + - - +
88A LEU 2.9 6.1 + - - -
89A LEU* 3.0 30.4 + - + +
90A PRO* 3.4 4.9 - - - +
118A HIS* 3.9 7.6 - - + +
122A ASP* 4.7 10.7 + - - -
126A HIS* 3.3 60.2 + + + +
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Residues in contact with CYS 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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47A ARG* 4.1 20.0 - - + -
51A LEU* 3.3 32.5 - - + +
79A VAL* 4.7 2.7 - - + -
84A TYR* 3.0 35.5 + - - +
85A VAL 2.8 1.4 + - - -
86A HIS* 1.3 93.2 - - - +
88A LEU* 1.3 59.1 + - - +
89A LEU 3.4 0.2 - - - -
90A PRO* 3.5 12.0 - - - +
91A PRO* 3.8 4.9 - - - +
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Residues in contact with LEU 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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51A LEU* 4.3 23.8 - - + -
72A LEU* 3.9 29.8 - - + +
75A PHE* 4.0 21.1 - - + +
76A THR* 4.1 31.6 - - - +
79A VAL* 4.5 11.7 - - + -
85A VAL* 2.8 18.1 + - - +
87A CYS* 1.3 80.6 - - - +
89A LEU* 1.3 65.1 + - - +
90A PRO* 3.4 1.3 - - - -
91A PRO* 3.0 19.8 - - + +
92A LEU* 3.2 16.2 + - + +
114A ILE* 4.2 18.6 - - + -
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Residues in contact with LEU 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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86A HIS* 3.0 19.2 + - + +
88A LEU* 1.3 77.9 - - - +
90A PRO* 1.3 56.4 - - + +
92A LEU* 3.2 3.7 + - - +
93A GLU* 2.6 39.6 + - - +
111A LEU* 3.8 23.3 - - + -
114A ILE* 4.1 11.0 - - + -
118A HIS* 3.9 22.7 - - + +
126A HIS* 3.7 42.8 - - + +
127A PHE* 4.2 9.6 - - + +
130A LEU* 4.1 18.0 - - + +
133A ARG* 5.6 3.8 - - - +
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Residues in contact with PRO 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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55A THR* 4.1 18.1 - - + +
86A HIS 3.4 9.9 - - - +
87A CYS* 3.5 8.3 - - - +
88A LEU 3.4 4.3 - - - -
89A LEU* 1.3 94.6 - - + +
91A PRO* 1.3 69.5 - - + +
93A GLU* 3.2 11.3 + - + +
94A SER* 3.0 21.5 + - - -
133A ARG* 6.1 2.5 - - - +
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Residues in contact with PRO 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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51A LEU* 4.8 14.4 - - + +
54A LEU* 4.4 11.5 - - + +
55A THR* 3.4 33.2 - - - +
68A LEU* 6.2 0.4 - - + -
72A LEU* 3.9 22.7 - - + -
87A CYS 3.8 5.8 - - - +
88A LEU* 3.0 31.4 - - + +
90A PRO* 1.3 93.9 - - + +
92A LEU* 1.3 59.1 + - - +
94A SER* 3.3 5.7 + - - -
95A LEU* 3.2 25.8 + - - +
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Residues in contact with LEU 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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69A ALA 4.1 4.5 - - - +
72A LEU* 4.0 33.2 - - + +
88A LEU* 3.2 18.0 + - + +
89A LEU 3.2 3.5 + - - +
91A PRO* 1.3 75.6 - - - +
93A GLU* 1.3 66.0 + - - +
95A LEU* 3.1 9.1 + - + +
96A ALA* 3.0 23.6 + - - +
107A ALA* 3.8 22.0 - - + +
110A SER* 3.9 30.3 - - - -
111A LEU* 3.7 22.4 - - + +
114A ILE* 3.7 30.1 - - + -
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Residues in contact with GLU 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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89A LEU 2.6 21.5 + - - +
90A PRO* 3.4 11.3 - - - +
92A LEU* 1.3 72.8 - - - +
94A SER* 1.3 63.6 + - - +
96A ALA* 3.2 13.7 + - - +
97A THR* 3.1 20.2 + - - +
111A LEU* 4.9 3.8 - - - +
130A LEU* 3.0 25.1 - - + +
133A ARG* 2.6 47.0 + - - +
134A LEU* 4.0 15.7 - - + +
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Residues in contact with SER 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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54A LEU 5.8 0.7 - - - -
55A THR* 3.5 24.7 + - - -
90A PRO 3.0 11.3 + - - -
91A PRO* 3.4 11.4 - - - -
93A GLU* 1.3 77.4 - - - +
95A LEU* 1.3 62.2 + - - +
97A THR* 3.3 19.1 + - - -
98A VAL* 3.8 9.9 + - - +
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Residues in contact with LEU 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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65A LEU* 4.0 37.5 - - + +
68A LEU* 4.0 19.1 - - + -
69A ALA* 3.5 36.1 - - + +
72A LEU* 4.1 9.4 - - + -
91A PRO 3.2 13.6 + - - +
92A LEU* 3.1 11.0 + - + +
94A SER* 1.3 74.7 - - - +
96A ALA* 1.3 56.6 + - - +
97A THR 3.1 9.0 + - - -
98A VAL* 3.6 21.9 + - + +
103A VAL* 3.9 10.8 - - + +
104A ARG* 3.7 13.3 - - - -
107A ALA* 3.9 11.2 - - + -
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Residues in contact with ALA 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 LEU 3.0 15.4 + - - +
93A GLU* 3.2 9.5 + - - +
95A LEU* 1.3 75.3 - - - +
97A THR* 1.3 60.4 + - - +
98A VAL 3.6 0.4 - - - -
104A ARG* 3.4 18.5 - - - +
107A ALA* 4.0 13.9 - - + -
108A VAL* 4.7 2.2 - - + -
111A LEU* 4.6 10.8 - - + -
134A LEU* 4.9 8.7 - - + +
141A THR 3.9 3.1 - - - +
142A SER* 4.6 1.2 - - - -
145A SER* 2.9 34.7 + - - +
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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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93A GLU* 3.1 14.6 + - - +
94A SER* 3.3 11.3 + - - -
95A LEU 3.1 1.2 - - - -
96A ALA* 1.3 80.7 + - - +
98A VAL* 1.3 66.2 + - - +
99A GLU* 3.9 1.2 + - - +
104A ARG* 4.3 0.2 - - - -
134A LEU* 4.3 8.1 - - - +
139A TRP* 5.0 10.7 - - + -
141A THR* 3.6 16.6 + - - +
142A SER* 3.3 26.5 + - - +
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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