Contacts of the strand formed by residues 109 - 118 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101G CYS* 4.3 2.9 - - + -
102G ASP 4.0 2.7 - - - -
103G VAL* 4.3 0.2 - - - -
108G ARG* 1.3 76.3 - - - +
110G LEU* 1.3 64.7 + - - +
111G ARG* 3.5 26.7 - - - -
112G GLY* 3.4 23.3 - - - -
128G GLU 5.9 0.4 - - - -
130G LEU* 3.6 20.2 - - + -
160G LEU* 3.4 31.2 - - + -
161G GLU* 3.9 32.1 - - + +
165G VAL* 3.6 26.1 - - + +
169G ARG* 4.6 0.6 - - - +
176J LYS* 3.2 30.7 + - - +
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Residues in contact with LEU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G SER* 4.5 9.4 - - - +
102G ASP* 2.9 20.9 + - + +
103G VAL* 4.0 8.1 - - - +
104G GLY* 3.9 24.9 - - - +
108G ARG 4.1 0.2 - - - +
109G PHE* 1.3 84.3 - - - +
111G ARG* 1.3 104.1 + - - +
128G GLU* 5.4 1.9 - - - +
107J TRP* 4.3 37.5 - - + -
173J GLU* 4.5 4.5 - - + +
176J LYS* 5.2 3.5 + - - +
180J GLN* 5.5 6.1 + - - +
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Residues in contact with ARG 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G CYS* 3.2 4.2 - - - -
102G ASP* 2.8 44.1 + - + +
109G PHE* 3.5 14.0 - - - -
110G LEU* 1.3 116.8 + - + +
112G GLY* 1.3 65.7 + - - +
113G TYR* 2.9 35.8 + - + +
128G GLU* 4.0 32.3 + - + +
105J SER 4.6 13.0 + - - -
106J ASP* 4.9 15.2 + - - +
107J TRP* 5.1 11.1 - - - +
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Residues in contact with GLY 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G GLY 3.6 7.4 - - - -
109G PHE* 3.4 17.4 - - - -
111G ARG* 1.3 80.5 - - - +
113G TYR* 1.3 70.3 + - - -
126G LEU 5.1 2.6 - - - +
127G LYS 5.1 1.7 - - - +
128G GLU* 5.2 6.4 + - - -
130G LEU* 3.8 25.9 - - - +
160G LEU* 4.3 6.1 - - - -
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Residues in contact with TYR 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G ARG* 3.0 39.9 + - - -
98G MET* 3.8 26.7 - - + -
99G TYR* 3.2 18.9 - - - +
100G GLY 3.0 15.4 + - - +
102G ASP* 3.2 14.8 + - - -
111G ARG* 2.9 44.5 + - + -
112G GLY* 1.3 77.7 - - - -
114G HIS* 1.3 66.9 + - - +
115G GLN* 3.5 19.1 - - - +
126G LEU* 5.2 3.1 - - - -
130G LEU* 5.5 0.2 - - - -
160G LEU* 3.6 11.6 - - - +
58H LYS* 6.5 1.6 - - - -
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Residues in contact with HIS 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G ARG* 2.9 40.1 + - - -
98G MET 3.3 7.0 - - - -
99G TYR* 3.9 13.1 - + - +
113G TYR* 1.3 78.7 - - - +
115G GLN* 1.3 63.9 + - - +
116G TYR* 3.7 16.6 - + - -
124G ILE 6.0 0.2 - - - -
125G ALA* 3.6 0.7 - - - -
126G LEU* 2.9 46.3 + - + +
133G TRP* 3.7 15.5 - + - -
147G TRP* 4.2 8.1 - + - -
152G VAL* 5.6 0.8 - - - +
156G LEU* 3.4 47.3 - - + +
160G LEU* 4.8 0.4 - - + -
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Residues in contact with GLN 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G ARG* 3.3 6.2 - - - +
98G MET* 3.0 55.5 + - - +
113G TYR* 3.5 27.3 - - - +
114G HIS* 1.3 83.3 + - - +
116G TYR* 1.3 65.6 + - - +
122G ASP* 5.4 2.9 + - - +
124G ILE 3.5 4.7 - - - +
125G ALA* 3.7 20.9 - - + -
126G LEU 4.7 3.7 - - - +
58H LYS* 5.3 7.1 + - - +
60H TRP* 3.4 25.2 - - + +
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Residues in contact with TYR 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G THR* 5.1 2.3 - - - +
74G HIS* 4.1 13.9 - - - -
77G ASP* 4.1 18.9 + - - -
95G VAL* 4.1 16.8 - - + -
96G GLN 3.2 12.1 - - - -
97G ARG* 3.1 51.9 + - + -
114G HIS* 3.7 11.0 - + - -
115G GLN* 1.3 78.0 - - - +
117G ALA* 1.3 60.8 + - - +
122G ASP* 4.0 1.9 - - - +
123G TYR* 3.0 27.4 + - + -
124G ILE* 2.8 27.2 + - + +
147G TRP* 3.5 32.1 - + - -
60H TRP* 3.7 8.2 - - - -
6I THR* 5.4 0.3 - - - -
7I THR 4.8 6.2 + - - -
9I ILE* 4.3 13.7 - - + -
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Residues in contact with ALA 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G LEU* 5.8 0.4 - - - +
94G THR 3.8 0.3 - - - +
95G VAL* 3.5 8.3 - - - +
96G GLN* 2.8 37.9 + - + +
116G TYR* 1.3 74.2 - - - +
118G TYR* 1.3 60.1 + - - +
119G ASP 4.2 0.7 - - - -
121G LYS 3.1 18.2 - - - +
123G TYR* 4.1 2.9 - - - +
60H TRP* 3.3 45.5 - - + -
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Residues in contact with TYR 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G LEU* 4.6 5.3 + - + -
81G LEU* 3.5 37.9 - - + -
82G ARG* 4.0 11.4 + - - +
85G TYR* 3.7 36.6 - + - +
87G GLN* 2.9 26.3 + - - -
93G HIS* 3.4 23.3 + - + +
94G THR 3.3 15.5 - - - -
95G VAL* 3.8 7.0 - - + -
117G ALA* 1.3 73.0 - - - +
119G ASP* 1.3 91.3 + - + +
120G GLY 3.1 0.2 - - - -
121G LYS* 2.9 25.7 + - - +
123G TYR* 4.1 20.7 - - + +
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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