Contacts of the helix formed by residues 139 - 144 (chain B) in PDB entry 3N1Q
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 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B GLU* 5.9 1.1 - - - -
55B ARG* 5.3 1.3 - - - +
135B HIS* 3.6 18.6 + - - +
136B ALA* 3.1 23.0 + - - -
137B GLN 4.4 0.2 - - - -
138B ASP* 1.3 80.3 - - - +
140B LEU* 1.3 64.8 + - - +
141B HIS* 3.0 28.8 + - - +
142B TYR* 3.2 25.0 + - - +
143B GLU* 4.3 6.4 - - - +
183B HIS* 5.1 1.9 - - - -
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Residues in contact with LEU 140 (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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54B GLU* 3.4 34.9 + - + +
55B ARG* 5.8 4.0 - - + -
60B SER* 3.6 20.6 - - - -
61B GLY 4.9 5.2 - - - +
62B PRO 4.7 1.1 - - - +
63B ALA* 4.2 17.7 - - + +
138B ASP 3.7 1.9 + - - +
139B SER* 1.3 71.4 + - - +
141B HIS* 1.3 64.2 + - - +
142B TYR 3.2 0.4 - - - -
143B GLU* 3.2 11.0 + - - +
145B ARG* 3.1 62.5 + - + +
146B ALA* 3.7 16.5 - - + +
183B HIS* 5.2 0.8 - - - +
185B SER* 3.5 15.3 - - - -
186B VAL 4.3 6.1 - - - +
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Residues in contact with HIS 141 (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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127B GLU* 3.4 33.8 + - + +
128B GLY 3.0 20.4 + - - +
129B TRP* 3.3 3.3 - - - -
130B ASP* 3.1 22.1 + - + -
135B HIS* 3.6 29.7 + + + +
139B SER* 3.0 18.1 + - - +
140B LEU* 1.3 79.0 - - - +
142B TYR* 1.3 56.8 + - - +
143B GLU 3.0 5.8 + - - -
144B GLY 3.3 9.4 + - - -
146B ALA* 3.4 19.6 + - + +
148B ASP* 3.7 5.6 - - - -
183B HIS* 3.2 20.7 - + - -
190B ZN 2.4 35.3 - - - -
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Residues in contact with TYR 142 (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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66B ARG* 3.5 59.7 + - + -
67B VAL* 2.9 34.8 + - - +
129B TRP* 3.6 4.4 + - - -
130B ASP* 3.0 38.6 - - + -
133B GLY* 3.0 17.2 + - - -
135B HIS* 2.6 51.5 + - + -
136B ALA 3.5 10.8 - - - -
137B GLN* 5.2 1.3 - - - -
138B ASP* 4.8 4.5 - - - -
139B SER* 3.2 25.8 + - - +
140B LEU 3.2 1.6 - - - -
141B HIS* 1.3 74.8 - - - +
143B GLU* 1.3 59.4 + - + +
144B GLY 3.8 0.4 - - - -
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Residues in contact with GLU 143 (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 ALA* 3.5 15.2 - - - +
64B GLU* 3.4 23.8 + - - +
65B GLY 2.9 21.1 + - - +
66B ARG* 5.0 0.2 - - - -
67B VAL* 3.7 20.2 - - + -
73B ARG* 2.9 21.2 + - - +
77B LEU* 4.2 6.4 - - - +
100B THR* 3.4 16.1 - - - +
129B TRP* 4.1 4.0 - - - -
138B ASP 5.6 0.2 - - - -
139B SER 4.3 5.7 - - - +
140B LEU* 3.7 17.0 - - - +
141B HIS 3.0 0.8 - - - -
142B TYR* 1.3 82.7 - - + +
144B GLY* 1.3 64.6 + - - +
145B ARG* 3.1 27.0 + - + +
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Residues in contact with GLY 144 (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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77B LEU* 4.5 2.5 - - - -
98B LEU 4.3 0.7 - - - -
99B MET* 3.5 19.1 - - - +
100B THR* 2.9 30.2 + - - +
103B CYS* 4.0 2.0 - - - +
128B GLY 5.0 0.7 - - - -
129B TRP* 3.6 27.6 - - - -
141B HIS 3.3 9.0 + - - -
143B GLU* 1.3 76.5 - - - +
145B ARG* 1.3 57.6 + - - +
146B ALA 3.6 3.1 - - - -
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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