Contacts of the helix formed by residues 105 - 116 (chain B) in PDB entry 2PWY
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 GLY 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B MET* 4.2 2.2 - - - -
102B THR 3.0 8.7 + - - -
103B GLY 3.5 0.6 - - - -
104B SER* 1.3 79.7 - - - +
106B GLY* 1.3 63.0 + - - +
107B LEU 3.6 1.3 - - - -
108B THR* 3.4 23.0 - - - -
109B LEU* 3.1 30.4 + - - +
134B ALA* 3.7 6.6 - - - +
138B VAL* 3.9 12.6 - - - +
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A SAH 3.1 13.5 + - - -
67B LEU* 3.4 44.9 - - - +
70B MET* 3.6 7.7 - - - +
76B PRO* 4.2 0.7 - - - -
104B SER 3.4 2.8 + - - -
105B GLY* 1.3 74.2 - - - +
107B LEU* 1.3 64.8 + - - +
109B LEU 3.2 9.4 + - - -
110B PHE* 3.4 10.0 + - - -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A SAH 2.9 17.4 + - - +
67B LEU* 4.4 0.8 - - - +
77B THR* 3.7 20.8 - - + +
82B ALA* 3.8 35.2 - - + +
85B MET* 3.8 36.1 - - + -
99B GLU* 3.5 19.1 - - + +
105B GLY 3.6 0.2 - - - -
106B GLY* 1.3 72.0 - - - +
108B THR* 1.3 62.6 + - - +
110B PHE* 3.0 7.5 + - + +
111B LEU* 2.9 44.5 + - + +
168B ALA* 4.1 13.2 - - + -
170B ASP* 4.6 8.1 - - + -
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Residues in contact with THR 108 (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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99B GLU* 2.8 29.6 + - - +
102B THR* 3.6 10.0 + - - +
105B GLY* 3.4 23.8 - - - -
107B LEU* 1.3 77.9 - - - +
109B LEU* 1.3 55.7 + - - +
111B LEU* 3.3 5.2 + - - +
112B ALA* 2.8 30.9 + - - +
121B VAL* 4.3 5.5 - - + +
123B SER* 4.5 1.3 - - - +
138B VAL* 4.1 14.6 - - + -
147B VAL* 3.9 33.2 - - + -
149B PHE* 4.4 5.2 - - + -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.6 22.7 - - + -
66B TYR* 3.7 36.3 - - + -
67B LEU* 4.2 5.6 - - + -
70B MET* 4.7 2.0 - - - -
105B GLY 3.1 20.2 + - - +
106B GLY 3.6 6.1 - - - +
107B LEU 3.2 0.4 - - - -
108B THR* 1.3 77.2 - - - +
110B PHE* 1.3 60.3 + - - +
112B ALA* 3.8 4.1 - - + +
113B ARG* 3.1 29.7 + - + +
137B ASN 4.3 4.7 - - - +
138B VAL* 4.1 22.7 - - + +
141B PHE* 4.2 10.1 - - + -
142B TRP* 3.6 35.2 - - + -
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Residues in contact with PHE 110 (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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87A THR* 3.9 34.1 - - + -
63B LEU* 3.6 35.4 - - + -
64B GLU 4.7 2.7 - - - -
67B LEU* 3.6 22.7 - - + -
79B PRO* 4.1 20.2 - - + -
82B ALA* 3.6 23.1 - - + -
83B SER* 3.9 17.3 - - - -
86B VAL* 4.0 17.4 - - + +
106B GLY 3.4 13.0 + - - -
107B LEU* 3.0 9.0 + - + +
109B LEU* 1.3 77.1 - - - +
111B LEU* 1.3 63.2 + - - +
113B ARG* 3.5 3.7 + - - +
114B ALA* 3.1 23.4 + - - +
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Residues in contact with LEU 111 (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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86B VAL* 4.3 6.3 - - + -
89B LEU* 4.0 18.6 - - + -
91B LEU* 3.6 22.9 - - + -
97B VAL* 4.1 9.4 - - + -
99B GLU* 3.7 46.0 - - + +
107B LEU* 2.9 27.3 + - + +
108B THR 3.6 5.2 - - - +
110B PHE* 1.3 76.0 - - - +
112B ALA* 1.3 62.4 + - - +
114B ALA* 3.2 6.7 + - - +
115B VAL* 3.1 28.1 + - - +
121B VAL* 3.8 18.8 - - + -
168B ALA* 4.0 11.9 - - + -
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Residues in contact with ALA 112 (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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108B THR 2.8 17.7 + - - +
109B LEU* 3.8 6.3 - - + +
110B PHE 3.3 0.2 - - - -
111B LEU* 1.3 74.5 - - - +
113B ARG* 1.3 64.4 + - - +
115B VAL* 4.2 0.2 - - - -
116B GLY 3.0 9.4 + - - -
121B VAL* 3.6 9.6 - - + +
138B VAL* 6.0 0.2 - - + -
142B TRP* 3.5 32.1 - - + +
146B ASN* 2.9 27.8 + - - +
147B VAL* 3.8 14.6 - - + -
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Residues in contact with ARG 113 (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 ASP* 2.9 40.4 + - - +
91A LEU 3.4 25.6 + - - +
92A ALA* 3.7 18.6 - - - +
93A PRO* 3.6 20.9 - - + +
95A MET* 5.3 2.0 - - - +
113A ARG 5.3 1.6 - - - +
114A ALA* 4.8 4.8 - - - +
63B LEU* 3.7 27.8 - - - +
109B LEU* 3.1 18.7 + - + +
110B PHE* 3.8 4.7 - - - +
112B ALA* 1.3 76.4 - - - +
114B ALA* 1.3 63.9 + - - +
115B VAL 3.4 0.3 + - - -
116B GLY* 3.5 6.1 + - - -
141B PHE* 3.5 28.7 - - - -
142B TRP* 4.1 28.3 - - + -
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Residues in contact with ALA 114 (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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113A ARG* 4.6 5.0 - - - +
114A ALA* 6.3 2.2 - - - +
86B VAL* 3.6 31.4 - - + -
91B LEU* 3.9 20.0 - - + +
92B ALA* 3.6 3.8 - - - -
93B PRO* 3.5 23.2 - - - +
110B PHE 3.1 11.7 + - - +
111B LEU 3.2 5.4 + - - +
113B ARG* 1.3 81.3 - - - +
115B VAL* 1.3 60.1 + - - +
116B GLY 3.7 0.2 + - - -
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.3 12.6 - - + -
92B ALA 3.9 6.7 - - - +
93B PRO* 3.4 3.2 - - - +
94B GLY 2.8 25.0 + - - -
95B MET* 3.4 35.0 - - + +
97B VAL* 4.0 17.7 - - + -
111B LEU 3.1 17.0 + - - +
112B ALA 3.8 0.2 - - - +
114B ALA* 1.3 78.8 - - - +
116B GLY* 1.3 65.2 + - - +
118B LYS 4.4 0.2 + - - -
119B GLY* 3.3 2.8 + - - -
120B LEU 3.6 20.2 - - - +
121B VAL* 3.9 11.7 - - + -
146B ASN* 3.8 14.6 - - - +
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO* 4.3 14.6 - - - -
93B PRO* 5.3 4.0 - - - -
112B ALA 3.0 15.3 + - - -
113B ARG 3.5 6.5 + - - -
114B ALA 3.4 2.4 - - - -
115B VAL* 1.3 75.9 - - - +
117B GLU* 1.3 59.1 + - - -
118B LYS 3.2 1.1 - - - -
119B GLY 3.0 16.3 + - - +
142B TRP* 5.0 0.9 - - - -
144B VAL* 4.7 0.9 - - - -
146B ASN* 2.7 24.2 + - - +
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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