Contacts of the strand formed by residues 123 - 134 (chain A) in PDB entry 1MM5
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 LEU 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLY 4.2 0.5 - - - +
112A VAL* 4.5 2.7 - - - -
113A THR* 3.3 28.9 + - - +
119A ASN 5.1 4.0 - - - +
120A TYR* 5.1 12.8 - - + -
121A ILE* 3.1 39.6 + - + +
122A PRO* 1.3 72.7 - - - +
124A PRO* 1.3 77.4 - - + +
125A VAL* 4.3 6.2 - - + +
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Residues in contact with PRO 124 (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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110A ALA* 5.5 6.3 - - + -
111A GLY 3.6 6.1 - - - +
112A VAL* 3.8 19.9 - - + -
122A PRO 4.5 2.0 - - - +
123A LEU* 1.3 91.7 - - + +
125A VAL* 1.3 73.5 + - - +
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Residues in contact with VAL 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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110A ALA* 3.1 6.6 - - - -
111A GLY* 2.7 61.1 + - - +
113A THR* 4.8 10.3 - - - +
123A LEU* 4.3 7.0 - - + +
124A PRO* 1.3 86.6 - - - +
126A LEU* 1.3 67.0 + - - +
127A LEU* 3.8 7.1 + - + -
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Residues in contact with LEU 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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108A PHE* 5.4 14.1 - - + -
109A THR 4.3 3.8 - - - +
110A ALA* 4.6 14.8 - - + +
125A VAL* 1.3 75.4 - - - +
127A LEU* 1.3 71.8 + - - +
128A PRO* 4.5 2.8 - - - +
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Residues in contact with LEU 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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108A PHE* 5.0 1.6 - - - -
109A THR 2.7 31.4 + - - +
111A GLY 5.6 1.6 - - - +
125A VAL* 3.8 9.8 + - + +
126A LEU* 1.3 83.5 - - - +
128A PRO* 1.3 60.8 - - + +
129A LEU* 2.7 26.1 - - + +
142A THR* 3.5 28.0 - - + -
144A ILE* 3.4 30.5 - - + -
155A PHE* 5.8 2.9 - - + -
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Residues in contact with PRO 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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107A GLY 3.6 6.1 - - - +
108A PHE* 3.6 30.5 - - + -
126A LEU 4.5 2.5 - - - +
127A LEU* 1.3 86.9 - - + +
129A LEU* 1.3 59.0 + - - +
142A THR* 3.3 18.5 - - - +
143A TYR* 3.1 70.0 + - + +
145A PRO* 4.0 14.8 - - + -
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Residues in contact with LEU 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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71A TYR* 3.3 31.0 - - + +
91A GLU* 5.6 4.7 - - - -
106A LEU* 3.7 2.6 - - - +
107A GLY 2.9 31.2 + - - +
109A THR* 3.4 31.4 - - - +
127A LEU* 2.7 33.4 - - + +
128A PRO* 1.3 75.1 - - - +
130A ALA* 1.3 65.3 + - - +
140A GLN* 3.3 14.8 - - - +
141A MET 3.2 9.2 - - - +
142A THR* 2.9 27.6 - - + +
143A TYR* 4.5 4.6 - - - -
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Residues in contact with ALA 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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91A GLU* 5.6 2.7 - - - -
105A GLY 3.3 17.3 - - - +
106A LEU* 3.5 21.8 - - + +
107A GLY 4.7 0.2 - - - +
129A LEU* 1.3 78.0 - - - +
131A SER* 1.3 65.6 + - - +
132A VAL* 4.2 2.2 - - + -
139A PHE 4.0 2.1 - - - +
140A GLN* 4.0 7.1 - - - +
141A MET* 2.8 46.0 + - + +
143A TYR* 5.1 1.3 - - + -
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A TRP* 5.0 11.1 + - - -
91A GLU* 3.8 18.3 + - - -
93A THR* 5.1 5.7 + - - -
103A HIS* 3.3 27.3 + - - +
104A LEU 3.8 0.2 - - - -
105A GLY 3.3 29.2 + - - -
106A LEU* 4.8 0.2 - - - +
130A ALA* 1.3 76.4 + - - +
132A VAL* 1.3 60.4 + - - +
138A THR* 6.1 2.5 - - - -
139A PHE 4.0 3.1 - - - -
140A GLN* 6.0 0.5 - - - +
159A ARG* 5.0 9.4 + - - -
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Residues in contact with VAL 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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102A PHE* 4.3 12.8 - - + -
103A HIS* 3.3 8.3 - - - +
104A LEU* 3.7 31.4 - - + -
105A GLY 5.6 0.4 - - - +
130A ALA* 5.7 2.0 - - + -
131A SER* 1.3 77.3 - - - +
133A GLY* 1.3 59.7 + - - +
139A PHE* 2.8 49.1 + - + +
141A MET* 4.9 19.1 - - + -
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Residues in contact with GLY 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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101A ASN 3.9 0.5 - - - +
102A PHE* 3.1 18.4 - - - -
103A HIS* 3.1 30.6 + - - -
132A VAL* 1.3 78.2 - - - +
134A TYR* 1.3 71.9 + - - -
137A VAL 3.1 13.2 - - - -
138A THR* 4.2 4.5 - - - -
139A PHE* 5.1 0.4 - - - -
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Residues in contact with TYR 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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99A ASP* 5.3 1.1 - - - +
101A ASN* 4.2 9.0 - - + -
102A PHE* 3.7 36.3 - + + +
103A HIS* 5.4 0.4 - - - -
133A GLY* 1.3 83.1 - - - +
135A GLY* 1.3 65.1 + - - +
136A PRO* 3.5 3.8 - - - +
137A VAL* 2.8 44.1 + - + +
138A THR* 5.0 0.8 + - - +
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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