Contacts of the strand formed by residues 124 - 130 (chain A) in PDB entry 2MPR
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 GLY 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ARG 5.7 0.9 - - - -
101A TRP* 5.2 1.0 - - - -
103A GLY 3.8 0.2 - - - +
104A LYS* 4.1 6.3 - - - -
105A ARG* 3.2 25.1 + - - +
122A ILE 3.7 1.0 + - - -
123A SER* 1.3 77.5 - - - +
125A PRO* 1.3 78.3 - - - +
126A GLY* 3.5 1.6 + - - -
144A THR* 4.6 4.4 - - - +
145A ARG 4.3 2.5 - - - -
73B ASP* 3.8 17.4 - - - +
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Residues in contact with PRO 125 (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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103A GLY 4.0 0.7 - - - +
104A LYS* 4.0 17.7 - - + +
124A GLY* 1.3 85.1 - - - +
126A GLY* 1.3 58.0 + - - +
144A THR* 3.2 2.9 - - - -
145A ARG* 3.0 51.0 + - + +
10B GLY 3.9 16.6 - - - +
11B ILE* 4.0 5.3 - - + +
70B GLN* 3.4 43.7 - - + +
71B GLN 4.4 0.4 - - - -
72B ASN 3.6 17.5 - - - +
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Residues in contact with GLY 126 (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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101A TRP* 3.5 8.1 - - - -
102A ALA* 3.5 0.7 - - - +
103A GLY 2.9 33.0 + - - -
124A GLY 3.5 0.2 + - - -
125A PRO* 1.3 76.1 - - - +
127A ALA* 1.3 63.6 - - - +
143A ALA 3.1 12.8 - - - -
144A THR* 4.1 6.7 - - - -
10B GLY 4.7 1.0 + - - -
11B ILE* 3.9 17.6 + - - +
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Residues in contact with ALA 127 (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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101A TRP* 3.2 25.5 - - - +
102A ALA* 4.1 2.2 - - + -
126A GLY* 1.3 76.1 - - - +
128A GLY* 1.3 60.3 + - - +
142A ALA* 3.5 2.8 - - - +
143A ALA* 3.0 32.0 + - + +
11B ILE* 4.1 6.3 - - + -
421B ALA* 3.6 31.0 - - + -
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Residues in contact with GLY 128 (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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100A ILE* 3.5 4.7 - - - +
101A TRP* 3.1 41.3 + - - +
127A ALA* 1.3 78.2 - - - +
129A ILE* 1.3 61.9 + - - +
141A LEU 3.2 13.0 - - - -
142A ALA* 4.0 2.2 - - - -
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Residues in contact with ILE 129 (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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92A ILE* 4.6 3.8 - - + -
95A LEU* 3.6 31.0 - - + -
98A SER* 3.7 23.1 - - - +
99A THR 3.3 11.4 - - - +
100A ILE* 3.9 18.4 - - + -
101A TRP* 5.0 0.2 - - - -
128A GLY* 1.3 75.4 - - - +
130A GLU* 1.3 62.6 + - - +
132A ILE* 4.0 18.4 - - + +
139A LEU 4.4 0.9 - - - +
140A SER* 3.4 1.9 - - - -
141A LEU* 2.9 49.0 + - + +
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Residues in contact with GLU 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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87A GLN* 4.8 1.2 - - - +
98A SER* 3.2 4.7 - - - -
99A THR* 2.8 57.8 + - - +
101A TRP* 4.4 4.9 - - + +
105A ARG* 2.8 43.1 + - - -
107A TYR* 4.0 8.2 - - + +
108A GLN* 2.9 23.9 + - - +
129A ILE* 1.3 75.7 - - - +
131A ASN* 1.3 79.8 + - - +
132A ILE 3.5 2.2 - - - -
140A SER* 3.4 18.8 - - - +
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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