Contacts of the strand formed by residues 109 - 118 (chain J) in PDB entry 3MGO
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 PHE 109 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101J CYS* 4.4 1.6 - - + -
102J ASP 3.9 5.2 - - - -
103J VAL* 4.0 5.9 - - - +
107J TRP 4.0 1.6 + - - -
108J ARG* 1.3 78.3 - - - +
110J LEU* 1.3 65.4 + - - +
111J ARG* 3.5 39.7 - - - -
112J GLY* 3.5 8.3 - - - -
130J LEU* 3.9 11.7 - - + -
160J LEU* 3.5 28.9 - - + -
161J GLU* 3.8 39.0 - - + +
165J VAL* 3.6 16.5 - - + +
169J ARG* 4.4 4.6 - - - +
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Residues in contact with LEU 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J SER* 4.8 6.1 - - - +
102J ASP* 2.8 21.4 + - + +
103J VAL 4.2 3.1 - - - +
104J GLY* 3.8 25.1 - - - +
108J ARG 4.1 2.9 - - - +
109J PHE* 1.3 84.1 - - - +
111J ARG* 1.3 95.7 + - - +
128J GLU* 5.1 3.3 - - - +
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Residues in contact with ARG 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J CYS* 3.3 2.6 - - - -
102J ASP* 2.7 55.1 + - + +
109J PHE* 3.5 14.4 - - - -
110J LEU* 1.3 117.8 + - - +
112J GLY* 1.3 63.9 + - - +
113J TYR* 2.6 36.9 + - + +
128J GLU* 4.1 31.5 + - + +
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Residues in contact with GLY 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J GLY 3.5 7.4 - - - -
101J CYS* 4.4 0.4 - - - -
109J PHE* 3.5 15.5 - - - -
111J ARG* 1.3 80.0 - - - +
113J TYR* 1.3 70.4 + - - -
126J LEU 5.3 1.9 - - - +
127J LYS 4.9 2.8 - - - +
128J GLU* 5.1 6.8 + - - -
130J LEU* 3.7 25.8 - - - +
160J LEU* 4.2 6.5 - - - -
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Residues in contact with TYR 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ARG* 3.0 42.9 + - - -
98J MET* 4.0 26.0 - - + -
99J TYR* 3.2 18.0 - - - +
100J GLY 2.9 15.1 + - - +
102J ASP* 2.8 16.5 + - - -
111J ARG* 2.6 46.5 + - + -
112J GLY* 1.3 78.2 - - - -
114J HIS* 1.3 66.6 + - - +
115J GLN* 4.0 16.6 - - - +
126J LEU* 5.2 3.6 - - - -
130J LEU* 5.3 0.4 - - - -
160J LEU* 3.5 12.2 - - - +
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Residues in contact with HIS 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J ARG* 3.1 36.3 + - - -
98J MET 3.3 6.7 - - - -
99J TYR* 3.7 15.7 - + - +
113J TYR* 1.3 78.1 - - - +
115J GLN* 1.3 65.5 + - - +
116J TYR* 3.5 22.7 - + - -
124J ILE 6.0 0.2 - - - -
125J ALA* 3.6 0.3 - - - -
126J LEU* 2.9 45.5 + - + +
133J TRP* 4.0 13.7 - + - -
147J TRP* 4.2 6.9 - + - -
152J VAL* 5.6 0.6 - - - +
156J LEU* 3.5 45.3 - - + +
160J LEU* 4.9 2.5 - - + -
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Residues in contact with GLN 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J ARG* 3.3 7.5 - - - +
98J MET* 2.8 57.0 + - - +
113J TYR* 4.0 18.4 - - - -
114J HIS* 1.3 84.9 - - - +
116J TYR* 1.3 65.6 + - - +
122J ASP* 5.2 3.6 + - - +
124J ILE 3.5 5.8 - - - +
125J ALA* 3.6 19.7 - - + +
126J LEU 4.8 4.1 - - - +
58K LYS* 5.1 9.7 + - - +
60K TRP* 3.5 24.7 - - + +
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Residues in contact with TYR 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J THR* 5.2 0.2 - - - +
74J HIS* 3.8 13.9 - - - -
77J ASP* 4.2 17.4 + - - -
95J VAL* 4.1 13.7 - - + -
96J GLN 3.3 11.7 - - - -
97J ARG* 3.0 52.4 + - + -
114J HIS* 3.5 12.8 - + - -
115J GLN* 1.3 79.5 - - - +
117J ALA* 1.3 61.3 + - - +
122J ASP* 3.9 2.4 - - - +
123J TYR* 2.9 28.2 + - + -
124J ILE* 2.8 31.7 + - + +
147J TRP* 3.5 33.4 - + - -
60K TRP* 3.8 5.9 - - - -
6L THR* 3.9 7.3 + - - -
7L THR 5.0 0.9 + - - -
9L ILE* 4.1 12.8 - - + -
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Residues in contact with ALA 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J THR 3.8 0.5 - - - +
95J VAL* 3.6 7.8 - - - +
96J GLN* 2.9 37.1 + - + +
116J TYR* 1.3 72.7 - - - +
118J TYR* 1.3 61.0 + - - +
120J GLY 4.5 1.3 - - - -
121J LYS 3.1 18.8 - - - +
123J TYR* 4.0 2.2 - - - +
60K TRP* 3.3 47.1 - - + +
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Residues in contact with TYR 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J LEU* 4.7 5.2 + - + -
81J LEU* 3.4 41.5 - - + +
82J ARG* 4.0 5.0 + - - +
85J TYR* 3.8 32.3 - + - +
87J GLN* 2.7 32.6 + - - -
93J HIS* 3.4 26.2 + - + +
94J THR 3.5 11.7 - - - -
95J VAL* 3.8 9.2 - - + -
117J ALA* 1.3 72.1 - - - +
119J ASP* 1.3 88.4 + - + +
120J GLY 3.2 0.9 - - - -
121J LYS* 2.8 26.2 + - - +
123J TYR* 4.0 18.6 - - + +
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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