Contacts of the helix formed by residues 127 - 138 (chain B) in PDB entry 2P82
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 SER 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLN* 3.8 2.7 - - - +
117B CYS 3.4 2.3 + - - -
118B PHE 4.4 0.7 - - - -
119B LEU 3.0 21.8 - - - -
121B ARG 2.9 30.2 + - - -
124B CYS 2.7 17.9 + - - -
125B CYS 3.5 1.0 + - - -
126B TYR* 1.3 81.6 - - - +
128B ILE* 1.3 66.6 + - - +
129B HIS* 3.7 5.8 - - - +
130B GLN* 3.2 20.3 + - - +
131B MET* 3.0 21.3 + - - +
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Residues in contact with ILE 128 (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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61B PHE* 3.9 12.1 - - + -
64B ILE* 4.5 4.5 - - + -
72B ASP* 3.6 38.1 - - + +
75B TRP* 4.4 9.0 - - + -
76B GLY* 4.5 1.1 - - - +
79B LEU* 3.7 35.2 - - + -
80B ARG* 3.8 17.5 - - - +
83B GLN* 3.6 9.3 - - - +
119B LEU 4.6 0.6 + - - -
120B ASP* 3.4 26.3 + - + +
127B SER* 1.3 71.2 - - - +
129B HIS* 1.3 77.9 + - + +
131B MET* 3.4 3.8 + - - +
132B ALA* 2.9 34.0 + - - +
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Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 3.4 26.4 - + - -
62B SER* 2.7 30.9 + - - -
63B PRO 4.6 1.6 - - - -
64B ILE* 3.6 34.1 - - + +
65B GLY 5.1 1.1 - - - -
120B ASP 3.2 33.5 - - - -
121B ARG* 3.8 1.8 + - - -
122B LYS* 3.8 30.1 - - + -
127B SER* 3.7 7.9 - - - +
128B ILE* 1.3 82.9 - - + +
130B GLN* 1.3 58.5 + - - +
132B ALA* 3.9 1.6 - - - +
133B GLN* 2.9 31.2 + - - +
291D GLU* 6.1 0.7 - - - -
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Residues in contact with GLN 130 (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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122B LYS* 2.6 30.5 + - - +
124B CYS 3.4 13.2 - - - +
125B CYS* 3.5 22.7 - - - +
127B SER* 3.2 20.1 + - - +
129B HIS* 1.3 79.6 - - - +
131B MET* 1.3 58.1 + - - +
133B GLN* 3.7 9.6 - - - +
134B MET* 2.9 34.0 + - - +
158B LEU* 3.8 14.9 - - + +
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Residues in contact with MET 131 (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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79B LEU* 3.6 39.3 - - + +
83B GLN* 3.5 33.4 - - - +
126B TYR* 4.0 8.1 - - - +
127B SER 3.0 15.9 + - - +
128B ILE* 3.8 4.3 - - - +
130B GLN* 1.3 74.5 - - - +
132B ALA* 1.3 59.9 + - - +
134B MET* 3.4 3.1 + - - +
135B GLY* 3.0 24.6 + - - -
146B PHE* 4.6 2.6 - - - -
151B VAL* 3.7 27.1 - - + -
154B VAL* 3.8 18.4 - - + +
155B LEU* 3.9 21.8 - - + -
158B LEU* 3.5 18.6 - - + -
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Residues in contact with ALA 132 (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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64B ILE* 4.5 5.6 - - + -
75B TRP* 4.2 28.5 - - + -
79B LEU* 4.0 7.1 - - + +
128B ILE 2.9 19.2 + - - +
129B HIS 3.9 2.7 - - - +
131B MET* 1.3 75.6 - - - +
133B GLN* 1.3 62.9 + - - +
135B GLY* 3.2 10.8 + - - -
136B VAL* 3.4 8.8 + - - +
140B LYS 4.6 1.6 - - - +
142B ILE* 3.7 30.2 - - + +
146B PHE* 5.5 3.3 - - - -
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Residues in contact with GLN 133 (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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188A VAL* 6.4 0.4 - - - +
221A LYS* 5.8 5.7 - - - +
64B ILE* 5.1 2.9 - - + +
65B GLY* 5.3 5.5 - - - -
129B HIS 2.9 19.8 + - - +
130B GLN* 3.7 13.2 - - - +
132B ALA* 1.3 76.0 - - - +
134B MET* 1.3 61.6 + - - +
136B VAL* 3.2 39.5 + - - +
137B GLY 3.8 2.3 + - - -
142B ILE* 3.4 22.0 - - - +
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Residues in contact with MET 134 (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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160A LEU* 4.1 21.5 - - + -
130B GLN* 2.9 21.6 + - - +
131B MET 3.7 4.7 - - - +
133B GLN* 1.3 72.9 - - - +
135B GLY* 1.3 65.5 + - - +
137B GLY* 3.1 16.4 + - - +
138B GLU* 3.5 11.3 + - - +
154B VAL* 3.9 25.8 - - + +
157B LYS* 3.8 39.3 - - + -
158B LEU* 3.8 22.0 - - + -
161B PHE* 3.9 25.1 - - + -
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Residues in contact with GLY 135 (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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131B MET 3.0 14.8 + - - -
132B ALA 3.2 5.8 + - - -
133B GLN 3.2 0.8 - - - -
134B MET* 1.3 76.1 - - - +
136B VAL* 1.3 55.5 + - - +
138B GLU* 2.9 24.5 + - - +
139B GLY 3.3 0.2 + - - -
140B LYS* 3.1 23.0 + - - +
146B PHE* 4.0 16.6 - - - -
154B VAL* 3.8 13.8 - - - +
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Residues in contact with VAL 136 (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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184A LYS 3.4 22.7 - - - +
185A MET* 3.6 24.8 - - + +
187A ARG 5.1 3.8 - - - +
221A LYS* 6.0 1.8 - - + -
132B ALA 3.4 1.7 + - - +
133B GLN* 3.2 26.3 + - - +
135B GLY* 1.3 75.5 - - - +
137B GLY* 1.3 56.5 + - - +
139B GLY* 2.9 20.4 + - - -
140B LYS 3.2 17.9 + - - +
141B SER* 4.5 1.3 - - - -
142B ILE* 3.7 37.9 - - + +
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Residues in contact with GLY 137 (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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156A LYS* 2.8 34.2 + - - -
160A LEU* 6.2 3.6 - - - -
185A MET* 3.4 16.5 - - - +
133B GLN 3.8 2.0 + - - -
134B MET* 3.1 14.7 + - - -
136B VAL* 1.3 77.7 - - - +
138B GLU* 1.3 61.1 + - - +
139B GLY 3.3 1.6 - - - -
157B LYS* 6.3 1.1 - - - -
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Residues in contact with GLU 138 (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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156A LYS* 4.3 2.2 - - - -
181A ASP* 5.7 1.4 - - - -
185A MET* 4.6 2.7 - - - -
134B MET 3.9 10.5 - - - +
135B GLY 2.9 10.2 + - - +
137B GLY* 1.3 80.6 - - - +
139B GLY* 1.3 60.3 + - - +
140B LYS* 3.4 13.1 + - - +
150B THR* 4.0 26.8 - - + +
153B GLN* 3.9 23.1 - - + +
154B VAL* 4.3 12.3 - - + +
157B LYS* 2.6 42.2 + - - +
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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