Contacts of the strand formed by residues 129 - 141 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A SER 3.5 2.5 - - - -
113A TYR* 3.3 31.4 + + + -
126A ALA* 3.2 19.9 + - + +
127A ARG 3.4 1.3 + - - +
128A ASP* 1.3 81.1 - - - +
130A ASP* 1.3 73.9 + - - +
131A ILE* 3.5 32.1 - - + -
160A LYS* 2.6 56.1 + - + -
163A PHE* 3.7 31.0 - + - -
173A ASN 4.2 13.0 - - - -
174A GLN* 3.8 25.4 - - + +
175A PHE* 3.1 41.9 + + - +
176A LEU* 4.2 2.0 - - + +
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Residues in contact with ASP 130 (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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111A GLY* 3.5 0.3 - - - -
112A SER* 2.8 39.5 + - - +
129A TRP* 1.3 87.8 + - - +
131A ILE* 1.3 64.9 + - - +
132A LEU* 3.8 15.2 - - + +
158A SER* 2.4 35.1 + - - -
160A LYS* 3.7 21.9 + - - +
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Residues in contact with ILE 131 (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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109A LEU* 3.5 35.0 - - + -
110A VAL 3.6 17.5 - - - +
111A GLY* 4.1 3.4 - - - +
129A TRP* 3.5 28.5 - - + -
130A ASP* 1.3 78.3 + - - +
132A LEU* 1.3 56.0 + - - +
158A SER* 3.5 3.6 - - - -
159A LEU* 2.8 35.3 + - + +
160A LYS* 3.7 22.4 - - + +
175A PHE* 3.5 47.8 - - + +
176A LEU* 4.3 8.3 - - - -
177A GLY 4.7 0.2 - - - +
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Residues in contact with LEU 132 (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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83A ILE* 5.2 1.1 - - + -
84A LYS 5.6 1.3 - - - +
94A VAL* 4.4 14.6 - - + -
108A VAL 3.7 0.9 - - - +
109A LEU* 3.5 7.3 - - - +
110A VAL* 2.8 48.1 + - + +
112A SER* 3.7 28.5 - - - +
130A ASP* 3.8 20.2 - - + +
131A ILE* 1.3 82.3 - - - +
133A LEU* 1.3 60.1 + - - +
134A ALA 4.3 0.6 + - - -
156A PRO* 3.9 27.6 - - + -
157A VAL 3.3 5.2 - - - +
158A SER* 3.8 19.7 - - - +
159A LEU* 4.9 0.4 - - - -
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Residues in contact with LEU 133 (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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107A TYR* 4.2 22.0 - - + -
108A VAL 3.4 21.8 - - - +
109A LEU* 4.1 5.8 - - + +
132A LEU* 1.3 71.9 - - - +
134A ALA* 1.3 63.5 + - - +
135A VAL* 4.8 6.3 - - + +
155A SER 4.3 1.6 - - - +
156A PRO* 3.4 2.3 - - - +
157A VAL* 2.9 38.5 + - + +
159A LEU* 4.0 19.7 - - + +
192A TYR* 3.7 28.7 - - + +
214A GLY 3.9 22.0 - - - +
217A TRP* 4.0 21.8 - - + +
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Residues in contact with ALA 134 (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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82A ALA 4.9 0.4 - - - +
83A ILE* 3.8 32.6 - - + +
106A LEU 3.3 1.7 - - - +
107A TYR* 3.7 0.2 - - - -
108A VAL* 2.9 35.2 + - + +
132A LEU 4.3 0.4 - - - -
133A LEU* 1.3 72.7 - - - +
135A VAL* 1.3 67.1 + - - +
153A TRP* 4.7 8.5 - - + -
154A GLY 4.2 15.9 - - - +
155A SER 4.9 1.1 - - - -
156A PRO* 4.3 12.6 - - + -
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Residues in contact with VAL 135 (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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105A LYS* 3.9 38.8 - - + -
106A LEU 3.1 5.8 - - - +
107A TYR* 3.8 26.5 - - + -
133A LEU* 4.8 9.2 - - + +
134A ALA* 1.3 79.8 - - - +
136A GLY* 1.3 64.3 + - - +
137A GLU* 4.1 5.7 + - - +
152A LYS 3.6 1.7 - - - +
153A TRP* 4.1 2.7 - - - -
154A GLY* 2.9 30.6 + - - +
155A SER 5.4 0.6 + - - -
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Residues in contact with GLY 136 (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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104A ASN 3.5 4.0 - - - +
105A LYS* 3.5 2.4 - - - -
106A LEU* 2.8 39.3 + - - +
135A VAL* 1.3 76.2 - - - +
137A GLU* 1.3 61.5 + - - -
138A VAL 3.7 0.4 + - - -
151A ILE* 4.2 8.7 - - - -
152A LYS 3.4 7.2 - - - -
153A TRP* 3.6 23.6 - - - -
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Residues in contact with GLU 137 (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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104A ASN* 3.8 12.4 - - + +
105A LYS* 2.5 51.5 + - - +
135A VAL* 4.1 7.0 + - - +
136A GLY* 1.3 70.5 - - - -
138A VAL* 1.3 62.3 + - - +
139A THR* 3.8 15.2 + - + +
150A SER 3.4 2.3 - - - +
151A ILE* 3.3 3.7 - - - -
152A LYS* 2.9 41.8 + - + +
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Residues in contact with VAL 138 (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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42A VAL* 3.8 27.4 - - + +
43A ASP* 5.6 1.3 - - + -
45A VAL* 4.1 29.2 - - + -
47A VAL* 5.1 1.8 - - + -
104A ASN* 3.0 36.9 + - - +
106A LEU* 3.7 30.1 - - + -
137A GLU* 1.3 74.2 - - - +
139A THR* 1.3 72.8 + - - +
140A LYS* 4.9 2.2 - - + -
149A ALA* 5.1 1.6 - - + -
150A SER 3.4 8.3 - - - +
151A ILE* 4.3 12.8 - - + -
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Residues in contact with THR 139 (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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104A ASN* 5.8 1.6 - - - +
137A GLU* 4.8 16.3 + - + +
138A VAL* 1.3 78.3 - - - +
140A LYS* 1.3 63.7 + - - +
148A THR 4.1 0.5 - - - +
149A ALA* 3.5 2.8 - - - +
150A SER* 2.9 43.7 + - - +
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Residues in contact with LYS 140 (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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43A ASP* 3.3 47.0 + - - +
44A GLY* 5.0 4.5 - - - -
45A VAL* 3.7 25.4 - - + -
138A VAL* 4.9 2.9 - - + -
139A THR* 1.3 79.0 - - - +
141A SER* 1.3 61.7 + - - +
142A THR* 5.9 1.2 - - + +
147A ILE* 4.4 27.6 - - + +
148A THR 3.4 5.6 - - - +
149A ALA* 4.7 3.8 - - + -
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Residues in contact with SER 141 (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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140A LYS* 1.3 74.5 - - - +
142A THR* 1.3 63.3 + - - +
143A ALA* 3.4 20.8 + - - +
146A LYS 3.0 3.6 - - - +
147A ILE* 3.3 3.8 - - - -
148A THR* 2.7 51.0 + - - -
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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