Contacts of the strand formed by residues 10 - 16 (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 GLY 10 (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* 3.4 0.2 - - - +
7M TYR* 3.2 31.5 + - - -
8M ASP 3.7 0.2 - - - -
9M ASN* 1.3 80.2 - - - +
11M VAL* 1.3 71.3 + - - +
110M VAL* 4.2 6.7 - - - -
116M GLN* 3.3 16.9 - - - +
191M ILE 3.1 12.6 - - - -
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Residues in contact with VAL 11 (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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5M MET 3.5 9.2 - - - +
6M LYS* 3.8 16.2 - - + -
7M TYR* 3.4 3.4 - - - -
10M GLY* 1.3 80.4 - - - +
12M ILE* 1.3 64.1 + - - +
108M ALA* 3.7 10.3 - - + -
109M GLY* 3.4 36.6 - - - +
116M GLN* 3.9 13.9 - - + -
117M PHE 4.0 10.3 - - - +
118M LEU* 4.7 6.5 - - + -
189M ALA 3.9 0.7 - - - +
190M ILE* 3.5 2.9 - - - -
191M ILE* 2.9 53.7 + - + -
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Residues in contact with ILE 12 (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* 3.1 5.6 - - - -
5M MET* 3.0 33.8 + - + +
7M TYR* 3.6 20.2 - - + -
11M VAL* 1.3 80.5 - - - +
13M ILE* 1.3 64.2 + - - +
161M VAL* 4.2 4.5 - - + +
164M ALA* 3.9 12.3 - - + -
165M GLU* 3.6 37.9 - - + +
168M ILE* 3.9 20.6 - - + -
188M LEU* 3.9 27.4 - - + -
189M ALA 3.4 10.3 - - - +
190M ILE* 4.4 13.7 - - + -
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Residues in contact with ILE 13 (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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2M VAL* 3.8 19.3 - - + -
3M ILE 3.3 12.6 - - - +
4M SER* 3.9 5.4 - - - -
12M ILE* 1.3 77.3 - - - +
14M ALA* 1.3 65.5 + - - +
33M LEU* 3.8 7.6 - - + +
41M VAL* 4.0 29.2 - - + +
42M VAL 4.8 0.2 - - - -
43M GLY* 3.9 10.3 - - - +
106M ILE* 3.7 42.2 - - + +
108M ALA* 4.1 17.3 - - + -
168M ILE* 5.3 0.4 - - - -
188M LEU* 3.5 1.9 - - - +
189M ALA* 2.9 40.1 + - + +
191M ILE* 4.9 2.0 - - + -
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Residues in contact with ALA 14 (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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2M VAL* 3.5 3.8 - - - +
3M ILE* 2.7 37.0 + - + +
13M ILE* 1.3 75.3 - - - +
15M ALA* 1.3 64.1 + - - +
33M LEU* 4.2 4.9 - - - -
168M ILE* 3.8 25.1 - - + -
172M MET* 4.2 15.9 - - - +
186M PHE* 4.3 3.1 - - + -
187M SER 3.4 14.6 - - - +
188M LEU* 4.0 9.9 - - + -
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Residues in contact with ALA 15 (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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1M SER 4.1 6.7 - - - +
2M VAL* 4.2 7.0 - - + -
14M ALA* 1.3 75.3 - - - +
16M ASP* 1.3 65.4 + - - +
17M ASN* 3.9 1.4 - - - +
31M GLU* 5.5 0.2 - - - +
32M ARG* 3.8 32.5 - - + +
33M LEU* 4.0 19.6 - - + +
172M MET* 4.1 4.0 - - - +
186M PHE* 3.7 4.0 - - - -
187M SER* 2.9 31.0 + - - +
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Residues in contact with ASP 16 (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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0M THR* 3.2 24.5 - - - +
1M SER 4.5 0.6 + - - -
15M ALA* 1.3 79.8 - - - +
17M ASN* 1.3 63.9 + - - +
18M LEU* 3.4 15.2 + - - +
30M VAL 3.9 2.4 - - - +
32M ARG* 2.7 44.8 + - - +
172M MET* 3.9 11.8 - - + +
182M SER* 3.2 6.5 - - - -
183M SER* 3.2 34.7 + - - +
185M ASN 3.6 8.1 - - - +
186M PHE* 3.4 12.8 - - + +
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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