Contacts of the helix formed by residues 88 - 99 (chain B) in PDB entry 2P3Z
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 ALA 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A PHE* 6.2 0.2 - - - -
67B LEU* 3.8 17.9 - - - +
68B GLY 3.1 4.9 + - - -
70B LEU* 3.8 16.4 - - + -
86B SER 3.8 1.8 + - - -
87B THR* 1.3 77.6 - - - +
89B GLY* 1.3 68.5 + - - +
90B GLU 3.4 1.6 + - - -
91B MET* 3.6 4.7 + - - +
92B GLY* 3.2 13.7 + - - -
132B LEU* 3.8 25.5 - - + +
135B ASN* 4.4 2.9 - - + -
136B THR* 3.7 23.1 - - - +
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Residues in contact with GLY 89 (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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17B PHE* 3.6 20.6 - - - -
67B LEU 3.1 16.6 + - - -
68B GLY 3.5 0.4 + - - -
69B THR 3.6 8.5 - - - -
70B LEU* 3.4 11.6 - - - +
88B ALA* 1.3 79.8 - - - +
90B GLU* 1.3 63.3 + - - -
92B GLY* 3.2 3.6 + - - -
93B CYS* 3.1 23.6 + - - -
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Residues in contact with GLU 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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90A GLU* 4.9 0.3 - - - +
94A PHE* 4.0 12.4 - - + -
403A TYR* 2.7 38.1 + - - +
17B PHE* 3.5 24.5 - - + +
22B THR* 2.5 41.4 + - - +
67B LEU 4.1 3.0 + - - -
88B ALA 3.4 1.0 + - - -
89B GLY* 1.3 70.2 - - - -
91B MET* 1.3 67.0 + - - +
93B CYS* 3.1 12.2 + - - +
94B PHE 3.2 8.3 + - - -
402B PRO* 4.0 24.5 - - + +
403B TYR* 3.6 14.9 + - + -
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Residues in contact with MET 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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91A MET* 3.3 51.6 - - + +
94A PHE* 3.6 34.6 - - + -
95A ILE* 3.4 27.6 - - + -
126A TYR* 4.4 2.5 - - + +
403A TYR* 5.4 1.3 - - - +
67B LEU* 3.5 31.9 - - + -
88B ALA 3.6 4.1 + - - +
89B GLY 3.5 0.4 - - - -
90B GLU* 1.3 76.4 - - - +
92B GLY* 1.3 64.3 + - - +
94B PHE* 3.0 18.1 + - - +
95B ILE* 3.1 11.6 + - - +
132B LEU* 3.7 22.4 - - + -
403B TYR* 5.8 0.4 - - - -
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Residues in contact with GLY 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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70B LEU* 3.8 8.3 - - - -
88B ALA* 3.2 16.8 + - - +
89B GLY 3.2 9.2 + - - -
91B MET* 1.3 78.1 - - - +
93B CYS* 1.4 60.5 + - - +
95B ILE* 3.2 2.6 + - - -
96B VAL* 3.0 27.0 + - - +
132B LEU* 4.6 1.4 - - - +
136B THR* 3.5 25.5 - - - +
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Residues in contact with CYS 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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15B ALA* 3.7 18.2 - - + +
16B TRP* 3.4 44.4 - - - -
17B PHE* 3.8 2.9 - - - -
70B LEU* 3.9 1.6 - - - -
89B GLY 3.1 16.2 + - - -
90B GLU 3.1 2.6 + - - +
92B GLY* 1.4 70.6 - - - +
94B PHE* 1.3 65.3 + - - +
97B GLU* 2.9 32.1 + - + +
402B PRO* 3.5 29.6 - - + -
403B TYR* 3.7 3.8 - - + -
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Residues in contact with PHE 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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20A GLY* 5.8 0.2 - - - -
21A ALA* 4.1 12.8 - - + -
22A THR* 3.6 28.0 - - + -
66A VAL* 3.6 30.3 - - + -
67A LEU* 4.5 8.7 - - + -
88A ALA 5.9 0.4 - - - -
90A GLU* 4.0 16.4 - - + -
91A MET* 3.4 42.4 - - + -
90B GLU 3.2 5.2 + - - +
91B MET* 3.0 11.8 + - - +
93B CYS* 1.3 76.0 - - - +
95B ILE* 1.3 60.4 + - - +
98B LYS* 2.9 46.4 + - + +
99B HIS* 5.9 0.7 - - + -
403B TYR* 3.4 42.1 - + + +
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Residues in contact with ILE 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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91A MET* 3.4 35.0 - - + -
132A LEU* 4.6 2.7 - - + -
91B MET 3.1 8.6 + - - +
92B GLY 3.2 5.6 + - - +
94B PHE* 1.3 79.4 - - - +
96B VAL* 1.3 63.6 + - - +
99B HIS* 3.0 21.0 + - - +
100B LEU* 3.0 29.2 + - + -
126B TYR* 3.7 18.6 - - + +
132B LEU* 4.6 5.8 - - + -
133B VAL* 3.9 35.7 - - + -
136B THR* 3.7 30.3 - - + +
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Residues in contact with VAL 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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13B VAL* 3.7 33.4 - - + -
14B ARG 4.7 2.5 - - - +
15B ALA* 3.9 20.2 - - + -
70B LEU* 4.6 0.2 - - + -
72B VAL* 4.0 23.8 - - + -
92B GLY 3.0 18.2 + - - +
95B ILE* 1.3 77.6 - - - +
97B GLU* 1.3 61.9 + - + +
100B LEU* 4.3 6.5 - - + -
101B ASN* 2.9 30.7 + - - +
104B ILE* 5.1 1.8 - - + -
136B THR* 3.5 19.1 - - + -
140B VAL* 4.0 12.3 - - + -
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Residues in contact with GLU 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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14B ARG* 3.4 2.5 - - - -
15B ALA* 2.8 28.2 + - + +
93B CYS* 2.9 25.1 + - + +
96B VAL* 1.3 73.9 - - - +
98B LYS* 1.4 61.3 + - + +
101B ASN* 3.1 11.1 - - - +
401B ARG* 2.8 37.8 + - - -
403B TYR* 3.3 33.5 - - + +
404B SER* 3.2 7.4 - - - -
405B HIS* 2.6 55.6 + - - +
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Residues in contact with LYS 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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21A ALA* 3.6 31.1 + - + +
22A THR* 4.1 23.2 - - + +
66A VAL* 3.8 8.0 - - - +
94B PHE* 2.9 43.4 + - + +
97B GLU* 1.4 82.1 - - + +
99B HIS* 1.3 59.4 + - - +
101B ASN* 3.8 3.6 - - - -
102B ARG* 3.7 14.3 + - - -
403B TYR* 4.0 17.5 - - + -
404B SER 2.9 29.1 + - - +
405B HIS* 4.8 3.8 - - + +
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Residues in contact with HIS 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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62A PHE 2.7 27.9 + - - -
63A GLY* 3.6 10.4 - - - -
66A VAL* 3.7 20.5 - - + +
94B PHE* 5.9 1.3 - - + -
95B ILE* 3.0 14.1 + - - +
98B LYS* 1.3 80.8 - - - +
100B LEU* 1.3 67.9 + - + +
101B ASN* 3.2 4.9 + - - +
102B ARG* 3.0 39.0 + - - +
103B PHE* 4.0 4.3 - + - -
122B ALA* 3.4 28.9 - - + +
123B THR* 3.9 10.8 - - + +
126B TYR* 2.8 37.7 + + - +
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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