Contacts of the helix formed by residues 138 - 152 (chain A) in PDB entry 4MSP
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 LYS 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A SER* 1.3 75.6 - - - +
139A ASP* 1.3 60.4 + - - +
141A VAL* 3.4 2.1 + - - +
142A LYS* 2.8 31.3 + - - +
165A VAL* 3.7 20.4 - - + +
166A GLU* 2.7 36.4 + - - +
169A PHE* 3.6 38.3 - - + -
173A ASP* 5.7 0.2 - - - -
178A GLY* 4.0 17.9 + - - +
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER* 3.1 7.9 + - - +
138A LYS* 1.3 82.3 - - - +
140A GLU* 1.3 58.1 + - - +
142A LYS* 3.4 26.5 + - - +
143A ALA* 2.9 28.9 + - - +
205B PGO 3.8 21.8 + - + +
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET* 3.4 22.2 - - - +
129A ASP* 3.8 1.0 - - - +
130A LEU* 3.6 21.6 - - + +
131A ASN* 2.9 27.2 + - - +
135A LYS 3.1 3.8 - - - +
136A LEU* 3.1 6.9 - - + -
137A SER* 2.9 36.5 + - - +
139A ASP* 1.3 76.8 - - - +
141A VAL* 1.3 62.2 + - - +
143A ALA* 3.3 5.9 + - - +
144A TYR* 3.0 22.9 + - - +
201A CA 2.5 30.8 - - - -
205B PGO 4.3 11.9 - - + -
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET* 3.8 26.9 - - + -
136A LEU* 4.0 17.3 - - + -
137A SER 3.1 14.0 + - - +
138A LYS 3.9 5.4 - - - +
140A GLU* 1.3 72.5 - - - +
142A LYS* 1.3 60.7 + - - +
144A TYR* 3.2 2.6 + - + +
145A LEU* 2.9 31.1 + - + +
165A VAL* 4.2 10.1 - - + -
168A ILE* 4.1 28.3 - - + -
169A PHE* 3.7 24.5 - - + -
180A ILE* 4.6 4.0 - - + -
204A 1PE 4.8 4.9 - - - +
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS 2.8 17.8 + - - +
139A ASP* 3.6 26.4 + - - +
141A VAL* 1.3 78.0 - - - +
143A ALA* 1.3 57.3 + - - +
145A LEU* 3.3 5.4 + - - +
146A LYS* 2.8 52.0 + - - +
158A GLU* 3.0 28.2 + - - +
161A HIS* 3.9 20.0 - - + -
162A ASP* 2.8 33.1 + - - +
165A VAL* 3.8 12.7 - - + +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 4.3 20.6 - - + -
139A ASP 2.9 17.5 + - - +
140A GLU 3.3 6.3 + - - +
142A LYS* 1.3 75.7 - - - +
144A TYR* 1.3 63.4 + - - +
146A LYS* 3.3 11.7 + - - +
147A LYS* 3.0 26.2 + - - +
20B HIS 4.8 6.5 - - - +
205B PGO 4.7 8.1 - - + +
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Residues in contact with TYR 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A SER* 5.6 2.9 + - - -
127A GLU* 3.5 31.1 + - + -
128A MET* 3.6 46.2 - - + -
140A GLU 3.0 13.2 + - - +
141A VAL 3.6 7.6 - - - +
142A LYS 3.2 0.2 - - - -
143A ALA* 1.3 74.5 - - - +
145A LEU* 1.3 66.4 + - + +
147A LYS* 3.3 17.8 + - - +
148A GLU* 3.0 46.0 + - + +
204A 1PE 3.9 26.9 - - - -
24B LYS* 3.5 17.3 + - - -
152B HIS* 3.6 25.1 + + - -
203B PGO 4.6 3.3 + - - -
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 2.9 18.6 + - + +
142A LYS* 3.6 4.3 - - - +
144A TYR* 1.3 77.3 - - + +
146A LYS* 1.3 58.5 + - - +
148A GLU* 3.3 2.0 + - - -
149A PHE* 2.8 41.2 + - + -
161A HIS* 3.9 18.4 - - + +
164A LEU* 4.0 25.4 - - + -
165A VAL* 3.9 26.5 - - + -
168A ILE* 4.3 9.4 - - + -
204A 1PE 3.5 44.0 - - - +
149B PHE* 4.3 12.6 - - + -
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Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LYS* 2.8 39.4 + - + +
143A ALA* 3.6 8.7 - - - +
144A TYR 3.2 0.4 - - - -
145A LEU* 1.3 77.1 - - - +
147A LYS* 1.3 61.9 + - - +
149A PHE* 3.4 1.7 + - - +
150A GLU* 3.0 24.7 + - - +
154A ALA 4.9 0.2 - - - +
158A GLU* 2.7 43.6 + - - -
161A HIS* 3.7 30.3 - - + +
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLU* 2.8 31.9 + - - +
143A ALA 3.0 15.5 + - - +
144A TYR* 3.4 24.7 - - - +
146A LYS* 1.3 77.4 - - - +
148A GLU* 1.3 66.2 + - - +
150A GLU* 3.5 13.9 + - - +
151A LYS* 3.0 26.9 + - - +
21B ARG* 4.6 29.5 - - + +
22B LYS 3.3 24.9 + - - +
24B LYS* 3.8 17.5 - - + +
27B ASP* 4.9 0.6 + - - -
117B ASN* 5.3 4.5 + - - +
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 4.9 1.9 + - - -
144A TYR* 3.0 44.6 + - + +
145A LEU 4.0 2.2 - - - +
147A LYS* 1.3 81.0 - - + +
149A PHE* 1.3 64.2 + - - +
151A LYS* 3.3 22.7 + - - +
152A HIS* 2.7 49.7 + - - -
204A 1PE 3.9 23.0 - - - +
24B LYS* 3.3 33.3 + - - +
148B GLU* 5.3 1.7 - - - +
152B HIS* 6.1 0.2 - - - +
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Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LEU* 2.8 37.5 + - + +
146A LYS 3.7 3.6 - - - +
148A GLU* 1.3 72.1 - - - +
150A GLU* 1.3 62.5 + - - +
152A HIS* 3.1 9.9 + - - +
153A GLY 3.2 0.5 + - - -
154A ALA* 2.9 45.5 + - + +
156A VAL* 4.0 10.5 - - + -
161A HIS* 3.4 25.4 - + + +
164A LEU* 3.6 25.6 - - + -
204A 1PE 3.7 39.0 - - - -
145B LEU* 4.3 5.6 - - + -
149B PHE* 4.2 11.4 - + - -
164B LEU* 3.5 33.7 - - + -
168B ILE* 5.7 0.2 - - + -
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS 3.0 17.6 + - - +
147A LYS* 3.7 12.5 - - - +
148A GLU 3.2 0.2 - - - -
149A PHE* 1.3 76.9 - - - +
151A LYS* 1.3 64.0 + - - +
153A GLY* 3.0 13.7 + - - -
154A ALA 3.4 11.2 + - - +
155A VAL* 4.4 17.4 - - + +
117B ASN* 4.8 14.4 - - - +
119B PRO* 3.3 33.8 - - + +
120B ARG* 5.2 1.1 + - - +
204B PGO 5.1 11.3 - - - +
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 4.4 12.5 - - - +
147A LYS 3.0 14.1 + - - +
148A GLU* 3.5 27.3 + - - +
149A PHE 3.2 0.2 - - - -
150A GLU* 1.3 76.1 - - - +
152A HIS* 1.3 85.9 + - + +
153A GLY 3.4 0.2 - - - -
24B LYS* 6.0 3.4 - - + +
117B ASN* 4.4 16.8 - - - +
118B GLY 5.7 0.7 - - - +
119B PRO* 3.9 12.6 - - + -
120B ARG* 2.9 26.4 + - - -
124B SER* 4.5 14.1 + - - +
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Residues in contact with HIS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 3.0 27.8 + - - -
148A GLU* 2.7 33.8 + - - +
149A PHE 3.1 1.8 + - - -
150A GLU 3.1 0.6 - - - -
151A LYS* 1.3 106.1 - - + +
153A GLY* 1.3 52.2 + - - +
154A ALA 3.5 1.8 - - - -
204A 1PE 3.6 31.0 - - - -
206A PGO 2.3 29.6 + - - -
120B ARG* 4.5 0.2 - - - -
124B SER* 3.9 23.6 + - - -
127B GLU* 4.7 0.2 + - - -
128B MET* 3.9 6.0 - - + +
144B TYR* 3.2 27.8 + + + -
148B GLU* 4.9 1.1 - - - -
185B PHE* 3.5 14.3 - - - -
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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