Contacts of the helix formed by residues 142 - 154 (chain B) in PDB entry 3NYN
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 PHE 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PHE* 4.8 5.6 - + - -
87B VAL* 4.0 34.3 - - + -
90B TYR* 3.8 45.5 - + - -
102B GLY* 4.3 19.1 - - - -
105B LEU* 4.5 15.3 - - + -
106B THR* 4.6 10.3 - - + -
110B LEU* 5.1 7.6 - - + -
129B CYS* 3.6 28.3 - - - -
133B LEU* 5.5 2.0 - - + -
141B LEU* 1.3 87.1 - - + +
143B GLN* 1.3 54.1 + - - +
144B GLU* 3.0 3.1 - - - -
145B LEU* 2.7 47.1 + - + -
146B THR* 3.1 9.6 + - - +
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Residues in contact with GLN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 5.8 0.6 - - - +
91B GLU* 6.1 0.4 - - - -
140B ASP* 3.4 33.1 + - + +
141B LEU 3.4 1.6 - - - -
142B PHE* 1.3 76.1 - - - +
144B GLU* 1.3 64.8 + - + +
146B THR* 3.9 10.9 - - + +
147B ARG* 3.1 44.3 + - - +
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Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.5 25.1 - - + +
140B ASP 6.1 0.4 - - - +
141B LEU 4.9 4.0 + - - +
142B PHE 2.7 5.0 + - - -
143B GLN* 1.3 79.1 - - + +
145B LEU* 1.3 64.8 + - + +
147B ARG* 2.6 43.9 + - - +
148B LEU* 3.2 29.5 + - + +
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Residues in contact with LEU 145 (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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83B PHE* 3.9 24.9 - - + -
110B LEU* 3.9 34.1 - - + -
117B LEU* 5.2 8.3 - - + -
118B ILE* 6.5 1.1 - - + -
121B VAL* 5.0 16.8 - - + -
125B LEU* 5.3 18.6 - - + +
126B VAL* 5.7 2.5 - - + -
129B CYS* 4.5 10.1 - - + -
142B PHE* 2.7 28.3 + - + +
144B GLU* 1.3 73.1 - - + +
146B THR* 1.3 56.4 + - - +
148B LEU* 3.1 15.9 + - + +
149B THR* 2.7 37.6 + - - +
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Residues in contact with THR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 4.4 2.4 - - - -
84B LEU* 4.1 16.5 - - + +
87B VAL* 3.8 29.0 - - + +
91B GLU* 5.3 2.8 + - - +
142B PHE 3.1 9.7 + - - -
143B GLN* 3.9 13.9 - - + +
145B LEU* 1.3 76.1 - - - +
147B ARG* 1.3 63.8 + - - +
149B THR* 3.7 4.9 - - - -
150B HIS* 3.0 44.9 + - + +
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 6.3 0.2 - - - +
143B GLN* 3.1 33.0 + - - +
144B GLU* 2.6 40.6 + - - +
145B LEU 3.2 0.2 - - - -
146B THR* 1.3 79.8 - - - +
148B LEU* 1.3 70.1 + - - +
150B HIS* 3.7 4.9 + - - +
151B GLU* 3.2 54.0 + - + +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 4.4 24.5 - - + +
121B VAL* 6.4 0.9 - - + -
122B PRO* 4.9 9.2 - - + -
125B LEU* 4.3 23.6 - - + -
144B GLU* 3.2 15.2 + - + +
145B LEU* 3.1 18.2 + - + +
147B ARG* 1.3 90.4 - - - +
149B THR* 1.3 60.4 + - - +
151B GLU* 3.2 19.8 + - + +
152B TYR* 2.9 29.3 + - - +
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Residues in contact with THR 149 (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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80B CYS* 4.1 35.2 - - + +
83B PHE* 3.9 14.1 - - + -
84B LEU* 4.1 28.0 - - + -
117B LEU* 4.5 9.0 - - + +
118B ILE* 4.6 8.1 - - + +
145B LEU 2.7 23.7 + - - -
146B THR 3.7 4.3 - - - -
148B LEU* 1.3 76.0 - - - +
150B HIS* 1.3 63.0 + - - +
152B TYR* 3.1 10.0 + - - +
153B LEU* 3.0 27.9 + - + +
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Residues in contact with HIS 150 (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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539A TRP 5.6 2.9 + - - -
53B TYR* 3.4 26.0 + + + -
58B GLU* 3.5 25.2 + - - -
84B LEU* 3.7 30.5 - - + +
146B THR* 3.0 41.9 + - + +
147B ARG* 4.0 5.2 - - - +
149B THR* 1.3 76.2 - - - +
151B GLU* 1.3 59.2 + - + +
153B LEU* 3.9 4.5 - - - +
154B SER* 2.9 34.1 + - - -
583B BU3 4.3 7.0 - - - -
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Residues in contact with GLU 151 (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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147B ARG* 3.2 42.5 + - - +
148B LEU* 3.2 22.2 + - + +
150B HIS* 1.3 76.9 - - - +
152B TYR* 1.3 60.6 + - - +
154B SER* 3.2 16.1 + - - +
155B VAL* 3.3 17.3 - - - +
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Residues in contact with TYR 152 (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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74B ARG* 4.9 3.8 + - - -
76B GLU* 4.3 15.3 - - + +
77B LEU* 4.0 15.1 - - + +
80B CYS* 4.0 19.1 - - - -
117B LEU 5.2 1.1 - - - -
118B ILE* 4.2 17.5 - - + -
119B PRO* 3.7 35.3 - - + +
148B LEU 2.9 13.0 + - - +
149B THR* 3.3 9.0 - - - +
151B GLU* 1.3 75.7 - - - +
153B LEU* 1.3 89.0 + - + +
155B VAL* 3.4 8.2 + - - +
156B ALA* 3.8 7.8 + - + -
157B PRO* 3.2 31.5 - - + +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.8 24.6 - - + +
67B PHE* 4.6 17.5 - - + -
71B CYS* 5.2 7.0 - - - -
77B LEU* 4.2 13.7 - - + +
80B CYS* 4.1 22.0 - - + -
81B VAL* 5.2 6.3 - - + -
84B LEU* 4.5 20.6 - - + -
149B THR* 3.0 20.2 + - + +
150B HIS* 4.0 1.8 - - - +
152B TYR* 1.3 98.6 - - + +
154B SER* 1.3 60.2 + - - +
155B VAL 3.0 10.5 + - - -
157B PRO* 3.6 5.9 - - + +
158B PHE* 3.1 24.9 + - - +
583B BU3 4.6 4.5 - - + -
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.6 38.8 - - - +
150B HIS 2.9 19.3 + - - -
151B GLU* 3.2 17.0 + - - +
153B LEU* 1.3 76.7 - - - +
155B VAL* 1.3 62.4 + - - +
158B PHE* 3.4 22.2 - - - +
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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