Contacts of the strand formed by residues 128 - 133 (chain M) in PDB entry 2FDB
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 VAL 128 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91M ASP* 4.1 13.2 - - + +
96M ARG* 3.9 28.9 - - + +
97M VAL 3.4 9.4 - - - +
98M ARG* 3.6 40.2 - - + +
124M GLY 4.0 4.0 - - - +
125M LYS* 2.9 19.7 + - + +
126M ASP 3.3 0.2 - - - -
127M CYS* 1.3 81.1 - - - +
129M PHE* 1.3 60.0 + - - +
143M ASN* 3.6 7.1 + - - -
144M ALA* 2.7 44.6 + - + +
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Residues in contact with PHE 129 (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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95M SER 3.5 1.0 - - - +
96M ARG* 3.3 2.7 - - - -
97M VAL* 2.8 41.6 + - + +
99M VAL* 4.8 7.9 - - + -
108M ILE* 3.5 24.7 - - + -
109M CYS 4.9 0.4 - - - -
110M MET* 4.1 17.3 - - + -
116M LEU* 4.4 9.2 - - + -
126M ASP 4.5 1.6 - - - -
127M CYS 4.0 8.1 - - - -
128M VAL* 1.3 79.0 - - - +
130M THR* 1.3 62.2 + - - +
131M GLU 3.7 0.3 + - - -
141M LEU* 3.6 36.3 - - + -
142M GLN 3.1 7.0 - - - +
143M ASN* 3.5 46.7 - - + -
144M ALA 4.2 0.4 - - - +
151M MET* 4.0 31.4 - - + -
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Residues in contact with THR 130 (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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94M GLY 3.4 21.5 - - - +
95M SER 3.5 3.4 - - - -
96M ARG* 3.5 28.8 + - + +
129M PHE* 1.3 72.2 - - - +
131M GLU* 1.3 68.2 + - - +
132M ILE* 3.4 17.0 + - + +
140M ALA 3.6 1.4 - - - +
141M LEU* 3.6 1.9 - - - -
142M GLN* 2.7 49.7 + - - +
144M ALA* 5.1 4.2 - - - +
2347P SER* 4.3 5.8 - - - -
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Residues in contact with GLU 131 (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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54M TYR* 4.7 5.1 + - - +
88M VAL* 6.0 0.3 - - - +
95M SER* 2.9 21.4 + - - +
97M VAL* 5.1 7.5 - - + +
129M PHE 3.7 1.6 + - - -
130M THR* 1.3 68.8 - - - +
132M ILE* 1.3 63.5 + - - +
133M VAL* 4.7 2.3 - - - +
139M THR* 4.2 11.2 + - + -
140M ALA 3.7 3.6 - - - -
141M LEU* 3.8 19.5 - - + +
176M LYS* 2.7 39.0 + - + +
2251P ARG* 4.2 6.9 + - - -
2284P ALA* 3.4 11.2 - - - +
2285P GLN* 2.8 38.0 + - - +
2347P SER* 2.8 28.1 + - - -
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Residues in contact with ILE 132 (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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130M THR* 3.8 16.8 - - + +
131M GLU* 1.3 78.4 - - - +
133M VAL* 1.3 70.6 + - - +
134M LEU* 3.6 22.4 + - + -
139M THR* 3.4 8.8 + - - +
140M ALA* 2.9 38.1 + - + +
142M GLN* 3.9 36.6 - - + +
150M TYR* 4.1 11.9 - - + -
167M GLN* 4.3 9.4 - - - +
2253P ARG* 6.2 0.2 - - - +
2347P SER* 4.2 5.4 - - - +
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Residues in contact with VAL 133 (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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131M GLU* 4.7 1.1 - - - +
132M ILE* 1.3 80.0 - - - +
134M LEU* 1.3 65.6 + - - +
137M ASN* 4.7 4.7 - - - +
138M TYR 3.8 2.9 - - - +
2251P ARG* 3.9 37.9 - - + +
2252P SER 3.7 22.0 - - - +
2253P ARG* 3.0 42.1 + - + +
2284P ALA* 3.9 28.0 - - + +
2347P SER* 4.7 1.6 + - - -
2348P ILE* 4.3 9.6 - - + +
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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