Contacts of the strand formed by residues 130 - 138 (chain A) in PDB entry 3MDS
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ARG* 3.9 5.5 - - - -
128A PHE 4.0 1.3 + - - +
129A GLY* 1.3 72.6 - - - -
131A GLY* 1.3 58.8 + - - +
149A PRO* 3.7 6.1 - - - +
150A ASN* 2.9 32.6 + - - +
168A TRP* 3.4 43.3 - - - +
169A GLU 5.3 1.1 + - - +
129B GLY* 3.6 4.9 - - - -
130B SER* 2.9 26.3 + - - -
150B ASN* 4.3 3.4 - - - +
169B GLU* 5.0 2.4 + - - +
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Residues in contact with GLY 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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127A ARG* 3.8 6.9 - - - +
129A GLY 3.9 2.0 + - - -
130A SER* 1.3 77.0 - - - +
132A TRP* 1.3 60.2 + - - -
148A THR 3.2 14.8 - - - -
150A ASN 3.7 10.5 - - - -
167A VAL* 2.8 37.0 + - - +
168A TRP* 3.4 12.0 - - - +
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Residues in contact with TRP 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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82A ASN* 3.5 45.7 - - + +
83A HIS* 3.7 14.8 - + - -
86A PHE* 3.8 24.2 - + + -
127A ARG* 4.4 0.4 - - - +
131A GLY* 1.3 80.6 - - - -
133A ALA* 1.3 57.9 + - - +
134A TRP* 3.5 36.1 - + + +
147A SER* 3.2 7.0 - - - -
148A THR* 3.0 33.1 + - - +
150A ASN 3.4 14.7 + - - -
151A GLN* 3.0 19.0 + - - -
164A GLY* 3.9 6.7 - - - -
165A ILE 3.3 15.5 - - - -
166A ASP* 3.5 56.3 + - + -
167A VAL* 4.1 4.5 - - - +
168A TRP* 3.9 1.6 - - - +
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Residues in contact with ALA 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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120A LEU* 4.3 16.3 - - + +
123A ALA* 4.2 4.5 - - + -
124A ALA* 3.6 42.8 - - + +
132A TRP* 1.3 74.2 - - - +
134A TRP* 1.3 60.8 + - - +
146A LEU 3.6 6.1 - - - +
147A SER* 4.2 2.0 - - - -
163A VAL 4.0 0.2 - - - +
164A GLY* 3.3 3.8 - - - -
165A ILE* 2.8 40.1 + - + +
167A VAL* 5.0 0.6 - - - +
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Residues in contact with TRP 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 ASN* 3.3 37.7 - - + -
85A LEU* 4.0 11.7 - - + -
120A LEU* 3.7 10.8 - - - +
132A TRP* 3.5 39.7 - + + +
133A ALA* 1.3 75.2 - - - +
135A LEU* 1.3 61.0 + - - +
136A VAL* 3.8 15.0 - - + -
144A HIS 3.7 0.2 - - - +
145A VAL* 3.2 6.6 - - - -
146A LEU* 2.8 43.1 + - + +
148A THR* 2.9 31.1 + - + +
152A ASP 4.1 3.8 - - - -
153A ASN* 3.8 5.8 - - - -
154A PRO* 3.4 24.5 - - + -
161A PRO* 3.9 28.0 - - + -
163A VAL 3.2 8.7 - - - -
164A GLY* 3.4 25.8 - - - -
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Residues in contact with LEU 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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102A LEU* 4.3 15.0 - - + -
106A ILE* 4.3 15.0 - - + -
110A PHE* 4.0 16.4 - - + -
116A LEU* 3.9 35.4 - - + -
120A LEU* 4.2 12.9 - - + +
134A TRP* 1.3 73.1 - - - +
136A VAL* 1.3 62.4 + - - +
143A LEU* 4.2 13.9 - - + -
144A HIS 3.5 11.9 - - - +
145A VAL* 4.0 2.5 - - + -
162A ILE* 2.9 36.1 + - + +
163A VAL* 2.9 29.1 + - + +
193A TRP* 4.6 1.8 - - + -
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Residues in contact with VAL 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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134A TRP* 3.8 11.2 - - + -
135A LEU* 1.3 78.8 - - - +
137A LYS* 1.3 58.9 + - - +
143A LEU* 3.2 12.0 - - - +
144A HIS* 2.9 49.5 + - + +
146A LEU* 4.0 10.3 - - + -
154A PRO* 3.7 33.7 - - + -
159A PHE* 3.6 32.5 - - + -
160A THR 3.3 9.6 - - - +
161A PRO* 3.9 11.0 - - + -
162A ILE* 4.2 3.4 - - - +
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Residues in contact with LYS 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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136A VAL* 1.3 74.3 - - - +
138A ASP* 1.3 76.0 + - - +
139A PRO* 5.7 1.3 - - - -
141A GLY* 4.0 20.2 + - - +
142A LYS 3.4 10.5 - - - +
143A LEU* 4.2 13.7 - - + -
144A HIS* 4.9 0.2 - - - -
159A PHE* 3.6 5.5 - - - -
160A THR* 2.9 40.8 + - - +
162A ILE* 4.2 9.4 - - + +
200A PHE* 3.9 32.0 + - + -
203A ALA* 3.4 31.9 + - - +
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Residues in contact with ASP 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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137A LYS* 1.3 90.4 - - - +
139A PRO* 1.4 71.2 - - + +
140A PHE* 2.8 32.9 + - + +
141A GLY 3.2 7.8 + - - -
142A LYS* 2.9 35.3 + - - +
144A HIS* 2.8 31.5 + - - +
159A PHE* 4.0 16.2 - - + +
160A THR* 5.8 1.6 - - - -
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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