Contacts of the strand formed by residues 103 - 113 (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 HIS 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A TRP* 5.8 13.4 - + + -
93A THR* 3.4 18.4 + - - +
94A TRP 3.8 6.1 - - - +
95A ARG* 5.4 3.6 - - + +
100A GLU 5.2 2.2 - - - +
101A ASN 3.1 14.8 + - - +
102A PHE* 1.3 77.3 - - - +
104A LEU* 1.3 60.9 + - - +
131A SER* 3.3 40.6 + - - -
132A VAL* 3.3 17.8 - - - +
133A GLY* 3.1 29.1 + - - +
134A TYR* 5.4 0.4 - - - -
138A THR* 4.8 14.7 + - + +
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Residues in contact with LEU 104 (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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93A THR* 4.3 1.8 - - - -
94A TRP* 2.9 38.9 + - + +
102A PHE* 4.5 19.9 - - + -
103A HIS* 1.3 75.0 - - - +
105A GLY* 1.3 77.8 + - - +
106A LEU* 4.8 8.5 - - + -
131A SER 3.6 3.1 - - - -
132A VAL* 3.7 26.7 - - + -
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Residues in contact with GLY 105 (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* 6.2 0.2 - - - -
92A SER 3.3 15.5 - - - -
93A THR* 4.1 4.0 - - - +
94A TRP 4.5 0.2 - - - -
104A LEU* 1.3 84.9 - - - +
106A LEU* 1.3 75.8 + - - +
130A ALA* 3.3 2.6 - - - +
131A SER* 3.3 27.9 + - - +
132A VAL* 5.6 0.2 - - - +
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Residues in contact with LEU 106 (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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90A TRP* 5.9 0.3 - - - -
91A GLU* 4.2 4.7 - - - +
92A SER* 2.8 31.5 + - - +
104A LEU* 4.8 9.2 - - + -
105A GLY* 1.3 84.6 - - - +
107A GLY* 1.3 58.8 + - - +
108A PHE* 6.0 0.7 - - + -
129A LEU 3.7 6.1 - - - +
130A ALA* 3.5 14.4 - - + +
131A SER 4.8 0.2 - - - +
143A TYR* 3.7 36.3 - - + +
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Residues in contact with GLY 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 3.5 8.1 - - - -
91A GLU* 3.5 18.3 - - - +
106A LEU* 1.3 77.6 - - - +
108A PHE* 1.3 78.0 + - - -
109A THR* 5.1 0.2 - - - -
128A PRO* 3.6 4.9 - - - +
129A LEU 2.9 28.8 + - - +
143A TYR* 4.2 2.1 + - - -
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Residues in contact with PHE 108 (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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89A GLY* 3.4 3.3 - - - -
90A TRP* 3.1 60.4 + + - +
91A GLU* 4.1 0.8 - - - +
106A LEU* 6.5 0.2 - - + -
107A GLY* 1.3 81.5 - - - -
109A THR* 1.3 63.9 + - - +
126A LEU* 5.4 13.2 - - + -
127A LEU 5.2 0.9 - - - +
128A PRO* 3.6 32.5 - - + -
143A TYR* 4.4 13.0 - + - -
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Residues in contact with THR 109 (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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69A GLY 3.7 14.4 - - - +
71A TYR* 3.3 25.4 + - + -
87A GLY* 3.7 1.6 - - - -
88A TYR 3.2 30.3 - - - +
89A GLY* 3.8 0.4 - - - +
91A GLU* 3.0 22.9 + - - +
108A PHE* 1.3 75.7 + - - +
110A ALA* 1.3 58.9 + - - +
111A GLY 3.8 1.8 + - - -
126A LEU* 5.1 2.9 - - - +
127A LEU* 2.7 39.7 + - - +
129A LEU* 3.4 22.5 - - - +
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Residues in contact with ALA 110 (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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86A ALA 3.2 3.6 - - - +
87A GLY* 3.2 4.3 - - - -
88A TYR* 3.1 35.8 + - + +
109A THR* 1.3 72.4 - - - +
111A GLY* 1.3 59.8 + - - +
112A VAL* 4.5 4.3 - - + +
124A PRO* 5.5 6.3 - - + -
125A VAL 3.1 18.2 - - - +
126A LEU* 4.5 14.1 - - + +
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Residues in contact with GLY 111 (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* 5.6 2.7 - - - -
85A ILE* 4.6 10.3 - - - -
86A ALA 3.2 9.9 - - - -
87A GLY* 4.0 3.1 - - - -
109A THR 3.8 3.4 + - - -
110A ALA* 1.3 73.0 - - - +
112A VAL* 1.3 60.0 + - - -
113A THR* 5.0 0.2 - - - -
125A VAL* 2.7 51.7 + - - +
127A LEU* 5.3 2.2 - - - +
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Residues in contact with VAL 112 (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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84A PRO 3.2 12.3 - - - +
85A ILE* 3.4 2.0 - - - -
86A ALA* 2.8 49.8 + - + +
110A ALA* 4.5 4.9 - - + +
111A GLY* 1.3 74.8 - - - -
113A THR* 1.3 62.0 + - - +
114A ALA* 3.7 1.7 + - + -
122A PRO* 6.0 4.0 - - + -
123A LEU 3.8 7.0 - - - +
124A PRO* 3.8 24.5 - - + -
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Residues in contact with THR 113 (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 GLU* 2.8 35.2 - - - +
84A PRO 3.5 2.7 - - - +
85A ILE* 3.3 27.1 - - + +
111A GLY 4.8 0.2 + - - -
112A VAL* 1.3 71.8 - - - +
114A ALA* 1.3 60.8 + - - +
115A ARG* 4.9 3.3 - - + +
120A TYR* 6.2 0.2 - - - -
121A ILE 4.5 0.9 - - - +
122A PRO* 3.2 18.2 - - - +
123A LEU 3.3 16.4 + - - -
125A VAL* 4.8 11.8 - - - +
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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