Contacts of the strand formed by residues 129 - 141 (chain B) in PDB entry 1MS4
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 TRP 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B SER 3.4 4.0 - - - -
113B TYR* 3.2 32.3 + + + -
126B ALA* 3.4 25.2 + - + +
127B ARG 3.4 3.7 + - - +
128B ASP* 1.3 78.6 - - - +
130B ASP* 1.3 76.5 + - - +
131B ILE* 3.8 16.2 - - + -
160B LYS* 2.9 47.7 + - + -
163B PHE* 3.6 33.0 - + + -
173B ASN 4.1 5.6 - - - -
174B GLN* 3.6 26.8 - - + +
175B PHE* 3.1 52.8 + + - -
176B LEU* 4.3 2.4 - - + +
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Residues in contact with ASP 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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111B GLY* 3.5 4.0 - - - -
112B SER* 2.8 39.7 + - - +
129B TRP* 1.3 85.1 + - - +
131B ILE* 1.3 73.5 + - - +
132B LEU* 3.7 17.7 - - + +
158B SER* 2.6 32.8 + - - -
160B LYS* 3.6 21.1 + - - +
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Residues in contact with ILE 131 (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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109B LEU* 3.6 31.9 - - + -
110B VAL 3.4 23.8 - - - +
111B GLY* 4.0 2.9 - - - +
129B TRP* 3.8 16.8 - - + -
130B ASP* 1.3 79.7 + - - +
132B LEU* 1.3 60.3 + - - +
158B SER* 3.4 4.7 + - - -
159B LEU* 2.8 34.7 + - + -
160B LYS* 3.5 30.1 - - - +
175B PHE* 3.5 48.2 - - + +
176B LEU* 4.4 7.2 - - - -
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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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83B ILE* 5.4 0.7 - - + -
84B LYS 5.8 1.6 - - - +
94B VAL* 4.4 13.2 - - + -
108B VAL 3.7 0.7 - - - +
109B LEU* 3.5 8.4 - - - +
110B VAL* 2.8 44.4 + - + +
112B SER* 3.7 29.8 - - - +
130B ASP* 3.7 25.1 - - + +
131B ILE* 1.3 84.7 - - - +
133B LEU* 1.3 59.6 + - - +
134B ALA 4.3 0.4 - - - -
156B PRO* 3.9 26.5 - - + -
157B VAL 3.3 4.5 - - - +
158B SER* 3.8 14.6 - - - +
159B LEU* 4.8 0.4 - - - -
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Residues in contact with LEU 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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107B TYR* 4.2 20.6 - - + -
108B VAL 3.5 26.2 - - - +
109B LEU* 4.1 6.5 - - + +
132B LEU* 1.3 74.1 - - - +
134B ALA* 1.3 64.3 + - - +
135B VAL* 4.4 7.6 + - + +
155B SER 4.3 1.6 - - - +
156B PRO* 3.3 2.0 - - - +
157B VAL* 2.9 39.0 + - + +
159B LEU* 4.0 16.6 - - + -
192B TYR* 3.9 21.8 - - + +
214B GLY* 3.7 23.3 - - - +
217B TRP* 3.9 18.6 - - + +
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Residues in contact with ALA 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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82B ALA 5.0 0.7 - - - +
83B ILE* 3.7 35.2 - - + +
106B LEU 3.4 1.4 - - - +
107B TYR* 3.7 1.9 - - - -
108B VAL* 2.9 34.0 + - + +
132B LEU 4.3 0.2 - - - -
133B LEU* 1.3 75.6 - - - +
135B VAL* 1.3 62.4 + - - +
136B GLY 4.2 0.2 - - - -
153B TRP* 4.6 9.0 - - + -
154B GLY 4.4 10.3 - - - +
155B SER 4.9 1.6 - - - -
156B PRO* 4.3 16.6 - - + -
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Residues in contact with VAL 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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105B LYS* 4.0 34.5 - - + -
106B LEU 3.0 7.9 - - - +
107B TYR* 4.1 24.0 - - + -
133B LEU* 4.9 9.9 - - + +
134B ALA* 1.3 78.5 - - - +
136B GLY* 1.3 64.7 + - - +
137B GLU* 4.1 9.0 + - - +
152B LYS 3.6 1.7 - - - +
153B TRP* 3.8 3.2 - - - -
154B GLY* 3.1 28.9 + - - +
155B SER 5.4 0.8 + - - -
215B LYS* 6.3 0.7 - - - +
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Residues in contact with GLY 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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104B ASN 3.6 0.9 - - - +
105B LYS* 3.4 6.8 - - - +
106B LEU* 2.7 37.3 + - - +
135B VAL* 1.3 76.3 - - - +
137B GLU* 1.3 62.1 + - - -
138B VAL 3.6 0.2 + - - -
151B ILE* 4.2 6.5 - - - -
152B LYS 3.5 5.6 - - - -
153B TRP* 3.6 27.1 - - - -
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Residues in contact with GLU 137 (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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104B ASN* 3.9 7.4 - - + +
105B LYS* 2.0 52.9 + - - +
135B VAL* 4.1 8.0 + - - +
136B GLY* 1.3 72.3 - - - -
138B VAL* 1.3 64.1 + - - +
139B THR* 3.7 13.6 + - + +
150B SER 3.4 2.6 - - - +
151B ILE* 3.3 4.2 - - - -
152B LYS* 2.9 41.9 + - + +
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Residues in contact with VAL 138 (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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42B VAL* 3.6 32.5 - - + +
43B ASP* 5.7 1.1 - - + -
45B VAL* 4.2 28.5 - - + -
47B VAL* 5.2 0.9 - - + -
104B ASN* 3.0 36.5 + - - +
106B LEU* 3.7 26.5 - - + -
137B GLU* 1.3 72.9 - - - +
139B THR* 1.3 72.4 + - - +
140B LYS* 4.9 2.2 - - + -
149B ALA* 4.9 1.6 - - + -
150B SER 3.3 8.5 - - - +
151B ILE* 4.1 12.6 - - + -
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Residues in contact with THR 139 (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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104B ASN* 6.3 0.2 - - - +
137B GLU* 3.7 14.4 + - + +
138B VAL* 1.3 78.3 - - - +
140B LYS* 1.3 66.6 + - - +
149B ALA* 3.3 4.5 - - - +
150B SER* 2.8 44.5 + - - +
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Residues in contact with LYS 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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43B ASP* 2.7 56.5 + - + +
44B GLY* 4.8 2.5 - - - -
45B VAL* 3.6 23.8 - - + -
138B VAL* 4.9 3.1 - - + +
139B THR* 1.3 82.0 - - - +
141B SER* 1.3 63.2 + - - +
142B THR* 5.9 0.7 - - + -
147B ILE* 4.6 23.3 - - + +
148B THR 3.3 6.1 - - - +
149B ALA* 4.4 5.2 - - + -
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Residues in contact with SER 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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140B LYS* 1.3 75.9 - - - +
142B THR* 1.3 61.5 + - - +
143B ALA* 3.1 24.6 + - - +
146B LYS 3.1 2.9 - - - +
147B ILE* 3.4 4.3 - - - +
148B THR* 2.7 44.6 + - - -
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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