Contacts of the helix formed by residues 141 - 154 (chain B) in PDB entry 4MDK
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 ASN 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B MET 5.4 1.2 + - - -
82B TRP* 3.5 23.9 - - - +
83B HIS 3.9 11.3 + - - +
84B PRO 3.0 7.4 + - - +
86B ILE 3.8 18.9 + - - +
87B TYR* 5.4 1.1 - - - -
88B GLU* 5.7 3.0 - - - +
139B PRO* 4.3 1.6 - - - -
140B ALA* 1.3 76.4 - - - +
142B VAL* 1.3 61.9 + - - +
143B ASP* 3.2 10.4 + - - +
144B ALA* 3.2 30.3 + - - +
145B SER* 3.0 26.5 + - - -
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Residues in contact with VAL 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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153A GLU* 4.1 38.6 - - + +
139B PRO* 4.0 22.9 - - + +
140B ALA 4.1 1.9 + - - +
141B ASN* 1.3 70.5 + - - +
143B ASP* 1.3 69.6 + - - +
145B SER* 3.6 4.8 - - - -
146B VAL* 2.7 46.2 + - + +
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Residues in contact with ASP 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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82B TRP* 3.7 22.6 - - + -
141B ASN* 3.2 5.3 + - - +
142B VAL* 1.3 90.5 - - - +
144B ALA* 1.3 55.5 + - - +
146B VAL* 3.7 5.8 + - - +
147B MET* 3.1 30.5 + - - +
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Residues in contact with ALA 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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82B TRP* 3.5 25.7 - - + +
83B HIS* 3.8 24.9 - - - +
84B PRO* 4.1 2.5 - - - -
141B ASN* 3.2 29.6 + - - +
142B VAL 3.2 0.4 - - - -
143B ASP* 1.3 78.6 - - - +
145B SER* 1.3 59.9 + - - +
147B MET* 3.4 1.0 + - - +
148B TYR* 2.9 30.1 + - - +
161B TYR* 3.4 5.5 - - + -
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Residues in contact with SER 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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149A ARG* 5.0 2.3 + - - -
84B PRO* 3.7 16.7 - - - +
136B THR* 3.4 30.9 + - - +
139B PRO* 3.5 22.6 - - - +
141B ASN 3.0 18.3 + - - -
142B VAL* 3.6 4.7 - - - -
144B ALA* 1.3 73.8 - - - +
146B VAL* 1.3 65.2 + - - +
148B TYR* 3.4 2.8 + - - +
149B ARG* 3.0 30.9 + - - +
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Residues in contact with VAL 146 (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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149A ARG* 4.2 26.2 - - - +
153A GLU* 4.4 11.7 - - - +
142B VAL* 2.7 28.1 + - + +
143B ASP* 3.9 6.3 - - - +
145B SER* 1.3 72.5 - - - +
147B MET* 1.3 66.5 + - - +
149B ARG* 3.1 12.5 + - - +
150B LYS* 3.0 21.0 + - + +
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Residues in contact with MET 147 (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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82B TRP* 3.9 18.6 - - - +
143B ASP 3.1 13.9 + - - +
144B ALA* 3.6 5.4 - - - +
146B VAL* 1.3 82.0 - - - +
148B TYR* 1.3 57.5 + - - +
150B LYS* 3.1 8.6 + - + +
151B TRP* 2.9 26.5 + - - +
160B GLU* 3.3 47.3 - - + +
161B TYR* 3.4 30.9 - - + +
164B ILE* 3.3 31.6 - - + -
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Residues in contact with TYR 148 (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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84B PRO* 4.2 5.6 - - + -
132B ASN 4.3 5.9 + - - -
134B PRO* 3.3 45.1 - - + +
136B THR* 4.4 11.4 - - + -
144B ALA 2.9 17.1 + - - +
145B SER 3.5 5.4 - - - +
147B MET* 1.3 76.1 - - - +
149B ARG* 1.3 59.8 + - - +
151B TRP* 3.1 37.5 + + - +
152B LYS* 2.8 47.0 + - + +
161B TYR* 3.7 33.1 - + + -
201B U94 4.0 16.7 + - - -
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Residues in contact with ARG 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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146A VAL* 5.5 6.9 - - - +
149A ARG* 2.8 53.4 - - - +
136B THR* 4.1 20.1 + - + -
145B SER* 3.0 21.7 + - - +
146B VAL* 3.1 8.5 + - - +
148B TYR* 1.3 76.8 - - - +
150B LYS* 1.3 61.7 + - - +
152B LYS* 3.2 28.7 - - - +
153B GLU* 3.1 50.9 + - - +
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Residues in contact with LYS 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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146B VAL* 3.0 13.7 + - + +
147B MET* 3.1 9.6 + - + +
149B ARG* 1.3 73.4 - - - +
151B TRP* 1.3 66.3 + - - +
153B GLU* 3.4 5.3 + - - +
154B SER* 3.1 26.7 + - - -
158B ASP* 4.5 14.8 - - - +
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Residues in contact with TRP 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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52B TYR* 4.2 14.3 + + - -
147B MET 2.9 13.5 + - - +
148B TYR* 3.1 50.2 + + - +
150B LYS* 1.3 76.3 - - - +
152B LYS* 1.3 76.2 + - + +
154B SER* 3.1 10.5 + - - -
156B GLY* 2.7 61.7 + - - -
158B ASP* 3.3 26.6 - - - +
159B ARG* 5.1 0.2 - - - -
161B TYR* 4.2 13.2 - - + -
162B THR* 3.3 27.8 + - + +
201B U94 3.6 45.3 - - - -
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Residues in contact with LYS 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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136B THR* 4.0 17.6 + - - +
148B TYR* 2.8 26.4 + - + +
149B ARG* 3.2 51.2 - - - +
150B LYS 3.3 0.2 - - - -
151B TRP* 1.3 91.1 - - + +
153B GLU* 1.3 74.4 + - + +
155B LYS* 3.0 22.9 + - - +
156B GLY 4.6 0.9 - - - +
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Residues in contact with GLU 153 (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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149B ARG* 3.1 48.6 + - - +
150B LYS* 4.1 4.5 - - - +
151B TRP 3.3 0.2 - - - -
152B LYS* 1.3 85.7 - - + +
154B SER* 1.3 57.7 + - - +
155B LYS* 2.9 12.6 + - - +
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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
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150B LYS 3.1 13.4 + - - -
151B TRP 3.1 8.5 + - - -
152B LYS 3.3 0.2 - - - -
153B GLU* 1.3 76.2 - - - +
155B LYS* 1.3 60.9 + - - +
157B LYS* 3.0 23.7 + - - +
158B ASP* 2.7 42.3 + - - +
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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