Contacts of the helix formed by residues 120 - 136 (chain B) in PDB entry 2NPP
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 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B SER 5.1 4.3 - - - +
49B PRO* 3.5 30.1 - - + +
119B ALA* 1.3 78.4 - - - +
121B TRP* 1.3 64.9 + - - +
122B PRO* 3.1 16.4 - - - +
123B HIS* 3.7 10.3 + - + +
124B LEU* 3.3 24.7 + - + +
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Residues in contact with TRP 121 (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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118B GLU* 3.3 16.9 + - + +
120B ALA* 1.3 76.8 - - - +
122B PRO* 1.4 62.8 - - + +
124B LEU* 2.9 20.3 + - + -
125B GLN* 2.4 69.4 + - + +
128B TYR* 3.5 36.8 - + - -
164B GLU* 5.0 4.7 - - + -
167B ARG* 2.9 81.7 - - + +
168B GLU* 3.5 19.3 - - + -
171B PHE* 4.1 12.3 - + - -
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Residues in contact with PRO 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 6.3 3.4 - - + +
120B ALA* 3.1 13.2 - - - +
121B TRP* 1.4 94.8 - - + +
123B HIS* 1.3 80.9 + - + +
125B GLN* 3.3 12.1 + - + +
126B LEU* 3.1 28.4 + - + +
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Residues in contact with HIS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 4.4 24.6 - - - -
57B GLU* 4.8 10.0 + - - -
59B LYS* 3.3 49.5 - - + +
60B ARG* 5.0 12.4 + - + +
63B LEU* 3.6 13.5 - - + +
92B ASN* 5.8 0.4 - - - +
120B ALA* 4.2 10.4 + - + +
121B TRP 3.4 0.6 - - - -
122B PRO* 1.3 86.7 - - + +
124B LEU* 1.3 68.1 + - + +
126B LEU* 3.2 4.8 + - - +
127B VAL* 2.8 27.7 + - + +
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Residues in contact with LEU 124 (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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92B ASN* 3.5 19.3 - - + +
93B MET* 3.3 32.5 - - + -
95B ARG* 4.1 13.9 - - - +
118B GLU* 3.9 27.6 - - + -
119B ALA 4.7 0.9 - - - +
120B ALA* 3.3 19.1 - - + +
121B TRP* 2.9 25.0 + - + +
123B HIS* 1.3 81.1 - - + +
125B GLN* 1.3 65.9 + - - +
127B VAL* 2.6 19.8 + - + +
128B TYR* 2.8 15.9 + - - -
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Residues in contact with GLN 125 (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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121B TRP* 2.4 70.3 + - + +
122B PRO* 3.6 10.4 - - - +
124B LEU* 1.3 67.2 - - - +
126B LEU* 1.3 63.8 + - + +
128B TYR* 3.3 3.9 + - - +
129B GLU* 2.8 48.6 + - - +
171B PHE* 3.9 16.0 - - + -
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Residues in contact with LEU 126 (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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60B ARG* 4.0 26.9 - - + +
63B LEU* 3.6 35.9 - - + -
64B SER* 4.1 15.5 - - - +
67B VAL* 4.9 6.4 - - + +
122B PRO* 3.1 16.7 + - + +
123B HIS* 3.4 6.7 - - - +
124B LEU 3.0 0.6 - - - -
125B GLN* 1.3 78.8 - - + +
127B VAL* 1.3 60.4 + - - +
128B TYR 3.0 1.6 - - - -
129B GLU* 4.3 17.9 - - + +
130B PHE* 2.7 39.0 + - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LYS* 5.1 0.9 - - - -
63B LEU* 4.2 7.9 - - + -
88B MET* 3.6 43.1 - - + -
89B PHE* 3.8 26.7 - - + -
92B ASN* 4.1 19.3 - - + +
93B MET* 4.4 5.8 - - - -
123B HIS* 2.8 28.4 + - + +
124B LEU* 2.6 15.7 + - + +
126B LEU* 1.3 71.7 - - - +
128B TYR* 1.3 55.9 + - - +
130B PHE* 3.9 5.4 - - - +
131B PHE* 3.0 30.5 + - - +
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Residues in contact with TYR 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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89B PHE* 3.9 26.9 - + - -
93B MET* 3.0 25.2 - - + +
121B TRP* 3.5 38.4 - + - -
124B LEU 2.8 14.6 + - - -
125B GLN 3.4 4.3 - - - +
127B VAL* 1.3 72.7 - - - +
129B GLU* 1.3 68.6 + - - +
130B PHE 3.0 0.7 - - - -
131B PHE* 2.8 7.8 + + + +
132B LEU* 2.7 25.1 + - - +
157B LEU* 5.5 0.4 - - + -
160B LEU* 4.2 2.6 - - - +
168B GLU* 2.6 35.5 + - + +
171B PHE* 3.1 30.5 - - + -
172B LEU* 3.4 30.4 - - + +
175B THR* 4.6 10.0 + - + +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 5.2 5.4 - - + -
125B GLN* 2.8 38.0 + - - +
126B LEU* 3.8 15.7 - - + +
128B TYR* 1.3 73.4 - - - +
130B PHE* 1.3 64.8 + - - +
132B LEU* 3.3 9.8 - - + +
133B ARG* 3.2 49.3 + - - +
171B PHE* 3.6 27.1 - - + -
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Residues in contact with PHE 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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63B LEU* 5.6 7.4 - - + +
66B MET* 3.5 59.5 - - + -
67B VAL* 3.8 21.0 - - + +
70B ILE* 3.9 18.2 - - + -
85B VAL* 3.2 37.5 - - + -
88B MET* 4.7 19.7 - - + -
89B PHE* 6.6 0.2 - - + -
126B LEU 2.7 23.6 + - - +
127B VAL* 3.9 6.3 - - - +
128B TYR 2.9 0.2 + - - -
129B GLU* 1.3 69.2 - - - +
131B PHE* 1.3 77.2 + + - +
132B LEU 2.7 3.0 + - - -
133B ARG* 2.9 8.8 + - + -
134B PHE* 2.8 26.5 + + + +
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 4.5 4.9 - - + -
86B VAL* 4.3 15.7 - - + -
89B PHE* 3.6 41.7 - + + -
127B VAL 3.0 17.5 + - - +
128B TYR* 2.8 7.8 + + - +
130B PHE* 1.3 82.1 - + + +
132B LEU* 1.3 61.6 + - - +
134B PHE* 2.7 46.5 - + - +
135B LEU* 3.7 6.8 + - + +
149B ILE* 4.3 12.8 - - + -
153B PHE* 3.7 31.2 - + - -
175B THR* 3.9 30.5 - - + -
179B ILE* 4.6 5.8 - - + -
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Residues in contact with LEU 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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128B TYR 2.7 11.3 + - - +
129B GLU* 3.3 12.1 - - + +
130B PHE 2.7 3.8 + - - -
131B PHE* 1.3 73.2 - - - +
133B ARG* 1.3 59.0 + - + +
134B PHE 2.7 13.3 + - - -
135B LEU 3.4 1.2 + - - -
136B GLU* 3.2 27.3 + - + +
171B PHE* 4.2 27.8 - - + -
174B THR* 3.9 27.1 - - + -
175B THR* 4.1 24.0 - - + +
178B ARG* 3.5 34.5 - - + +
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Residues in contact with ARG 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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67B VAL* 3.5 22.7 - - + +
68B GLU* 5.9 0.2 - - - +
70B ILE* 5.2 8.9 - - + +
71B THR* 3.2 44.4 + - - +
129B GLU* 3.7 32.1 + - - +
130B PHE* 2.9 11.4 + - + +
132B LEU* 1.3 77.0 - - + +
134B PHE* 1.3 67.6 + - - +
136B GLU* 3.2 24.8 + - + +
137B SER* 2.7 22.1 + - - +
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Residues in contact with PHE 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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70B ILE* 5.7 7.8 - - + +
82B TYR 5.7 0.7 - - - -
83B PRO* 5.7 4.0 - - + -
85B VAL* 3.2 50.3 - - + -
86B VAL* 4.6 10.5 - - + -
130B PHE* 2.8 17.0 + + + +
131B PHE* 2.7 45.3 - + - +
132B LEU 2.7 0.8 + - - -
133B ARG* 1.3 83.7 - - - +
135B LEU* 1.3 85.5 + - + -
136B GLU 3.0 2.6 + - - -
137B SER* 3.5 11.6 + - - -
140B PHE* 4.3 27.8 - + - +
144B ILE* 5.8 8.1 - - + -
145B ALA* 5.8 2.9 - - + -
149B ILE* 5.9 1.6 - - + -
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Residues in contact with LEU 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 PHE* 3.7 5.5 + - + +
132B LEU 3.4 3.9 + - - +
134B PHE* 1.3 116.6 - - + +
136B GLU* 1.3 55.9 + - - +
137B SER 3.3 4.9 + - - +
140B PHE* 3.2 30.3 - - + +
141B GLN 3.4 18.2 - - - +
142B PRO* 4.9 3.4 - - + -
144B ILE* 5.3 4.7 - - + -
145B ALA* 4.6 14.4 - - + +
149B ILE* 5.8 4.9 - - + -
178B ARG* 6.1 0.3 - - - +
182B LYS* 3.2 29.5 + - + +
183B PHE* 5.0 16.8 - - + -
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Residues in contact with GLU 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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132B LEU* 3.2 24.4 + - + +
133B ARG* 3.2 34.0 + - - +
134B PHE 3.0 3.4 + - - -
135B LEU* 1.3 79.5 - - - +
137B SER* 1.3 58.6 + - - +
138B PRO* 4.7 1.4 - - - +
178B ARG* 2.8 48.2 + - + +
182B LYS* 3.9 12.1 - - - +
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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