Contacts of the strand formed by residues 116 - 122 (chain M) in PDB entry 3SDI
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 GLN 116 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6M LYS* 3.9 25.6 + - + +
7M TYR 2.9 14.0 + - - +
8M ASP 2.9 29.5 + - - -
9M ASN* 4.4 1.1 - - - +
10M GLY* 3.3 30.6 - - - +
11M VAL* 3.9 11.4 - - + -
109M GLY 3.8 4.5 - - - -
110M VAL* 4.6 2.5 - - - +
111M GLN* 5.2 1.2 - - - +
114M GLY 4.9 4.9 - - - +
115M ASP* 1.3 80.4 - - - +
117M PHE* 1.3 59.6 + - - +
118M LEU 4.2 0.2 - - - -
153M GLU* 5.8 0.2 - - - +
156M ILE* 3.6 15.0 - - - +
193M LYS* 6.1 0.8 - - - +
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Residues in contact with PHE 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M VAL* 4.0 3.8 - - - +
80M PRO* 3.8 24.2 - - + -
81M SER* 3.7 27.6 - - - -
84M PHE* 3.6 34.3 - + + -
107M VAL* 3.7 20.0 - - + -
108M ALA* 3.4 5.0 - - - -
109M GLY 2.6 43.1 + - - +
111M GLN* 4.1 16.6 - - + +
115M ASP 3.6 0.2 + - - -
116M GLN* 1.3 74.9 - - - +
118M LEU* 1.3 63.0 + - - +
119M ARG* 3.7 33.7 - - + -
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Residues in contact with LEU 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M SER* 3.6 29.2 - - - +
5M MET* 4.1 12.3 - - - +
6M LYS* 3.7 19.9 - - + +
11M VAL* 4.7 9.6 - - + -
106M ILE* 3.9 8.1 - - + -
107M VAL 3.4 1.1 - - - -
108M ALA* 3.6 28.9 - - + -
116M GLN 4.2 0.8 + - - -
117M PHE* 1.3 76.4 - - - +
119M ARG* 1.3 59.8 + - - +
129M SER* 2.5 32.6 + - - -
130M SER 3.3 21.5 + - - +
131M PRO 4.0 14.1 - - - +
133M LEU* 3.7 16.3 - - + +
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Residues in contact with ARG 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L GLU* 2.7 30.5 + - - -
53L ASP* 4.6 5.5 + - - -
84M PHE* 3.4 44.4 - - + -
105M ILE 3.9 0.2 - - - +
106M ILE* 3.3 3.6 - - - +
107M VAL 2.8 37.9 + - - -
117M PHE* 3.7 21.8 - - + -
118M LEU* 1.3 76.1 - - - +
120M TYR* 1.3 68.3 + - - +
127M THR* 2.9 25.8 + - - -
128M TYR* 3.3 13.9 - - - +
129M SER* 3.2 27.0 - - - +
133M LEU* 3.6 4.9 - - - -
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Residues in contact with TYR 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M PHE* 3.6 3.6 - - - -
104M ALA* 3.8 10.9 - - + +
105M ILE 3.2 13.5 - - - -
106M ILE* 4.0 6.7 - - + +
119M ARG* 1.3 73.2 - - - +
121M VAL* 1.3 61.3 + - - +
122M ASN* 2.9 47.5 + - + +
126M VAL 3.9 4.0 - - - -
127M THR* 3.0 29.1 - - - -
128M TYR* 2.9 63.1 + + + +
133M LEU* 3.8 13.5 - - + -
134M ALA 4.5 8.1 - - - -
135M THR* 3.7 30.9 - - + -
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Residues in contact with VAL 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M PHE* 3.9 18.2 - - + -
87M LEU* 4.7 4.5 - - + -
88M ALA* 3.8 23.6 - - - +
91M MET* 3.8 26.5 - - + -
104M ALA* 3.6 0.2 - - - -
105M ILE* 2.6 60.5 + - + +
120M TYR* 1.3 78.4 - - - +
122M ASN* 1.3 70.0 + - - +
125M GLY* 4.1 5.2 - - - -
126M VAL 3.2 7.6 - - - +
127M THR* 3.8 18.4 - - + -
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Residues in contact with ASN 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M MET* 3.6 15.3 - - - +
103M ASN 3.4 13.7 - - - +
104M ALA* 4.0 3.8 - - + -
120M TYR* 2.9 36.7 + - + +
121M VAL* 1.3 78.6 - - - +
123M LEU* 1.3 66.2 + - + +
124M LEU* 2.7 28.0 + - - +
125M GLY* 2.7 31.0 + - - -
126M VAL* 3.4 18.4 + - - +
128M TYR* 5.2 0.6 + - - -
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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