Contacts of the strand formed by residues 180 - 186 (chain A) in PDB entry 4MXW
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A SER* 4.8 3.3 + - - +
98A SER* 4.2 20.3 + - - +
99A LEU 3.5 5.4 - - - -
100A LEU* 4.0 15.1 - - + +
137A LEU* 4.1 4.0 - - - +
138A PHE* 3.1 58.5 + - + +
178A GLY 3.5 8.9 + - - +
179A ASP* 1.3 80.1 - - - +
181A LEU* 1.3 63.7 + - - +
182A SER* 3.7 4.0 + - - -
57H GLY 4.2 8.5 + - - -
58H THR 3.6 22.4 + - - -
59H ASN* 3.9 20.1 - - - +
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 5.6 1.1 - - + -
98A SER* 3.3 3.1 - - - -
99A LEU* 2.7 56.4 + - + +
101A VAL* 4.3 13.7 - - + -
107A TYR* 6.2 0.2 - - + -
109A VAL* 3.9 24.9 - - + -
135A VAL* 5.0 1.8 - - + -
136A GLN 3.5 4.0 - - - +
137A LEU* 4.1 17.9 - - + -
148A LEU* 3.8 28.5 - - + -
175A LEU* 3.9 28.9 - - + -
180A GLN* 1.3 72.3 - - - +
182A SER* 1.3 60.2 + - - +
200A PHE* 3.9 16.9 - - + -
202A ALA* 4.7 4.5 - - + -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASN 4.2 10.5 - - - -
98A SER* 3.5 20.4 - - - -
135A VAL* 3.7 0.5 - - - +
136A GLN* 2.9 51.4 + - - +
138A PHE* 5.5 4.7 + - - +
145A HIS* 5.2 4.3 + - - -
180A GLN 4.5 3.4 + - - -
181A LEU* 1.3 73.7 - - - +
183A THR* 1.3 69.2 + - - +
200A PHE* 4.6 2.7 - - - -
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 4.6 4.0 - - - +
79A TRP* 2.9 35.3 + - + +
97A ASN* 5.0 4.3 + - - -
111A SER* 4.5 0.2 - - - +
133A HIS* 3.8 16.4 - - + -
134A GLU 3.2 5.6 - - - -
135A VAL* 3.4 32.5 - - + -
136A GLN* 4.7 1.8 - - - -
182A SER* 1.3 81.7 - - - +
184A HIS* 1.3 62.5 + - - +
185A THR* 4.2 3.8 + - - +
200A PHE* 3.6 24.9 - - + -
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Residues in contact with HIS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ALA* 5.0 0.3 - - - +
133A HIS* 3.9 0.5 - - - -
134A GLU* 2.9 45.5 + - + +
136A GLN* 3.3 27.5 - - - +
183A THR* 1.3 71.3 - - - +
185A THR* 1.3 68.7 + - - +
186A ASP* 3.9 24.2 + - - -
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 3.6 21.3 - - + -
113A VAL* 4.6 3.6 - - + -
115A PHE* 5.4 1.7 - - - -
132A ALA 3.5 13.0 - - - -
133A HIS* 2.9 34.8 - - + +
183A THR 4.4 3.1 - - - +
184A HIS* 1.3 87.2 + - - +
186A ASP* 1.3 66.6 + - - +
188A ILE* 2.8 37.5 + - + +
191A LEU* 4.1 9.2 - - - +
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Residues in contact with ASP 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.9 6.6 - - - -
130A TYR* 3.7 38.2 + - + +
131A LEU* 3.6 3.5 - - - -
132A ALA* 2.9 47.3 + - + +
184A HIS* 3.9 21.1 + - - -
185A THR* 1.3 77.0 - - - +
187A GLY* 1.3 61.2 + - - +
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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