Contacts of the strand formed by residues 172 - 177 (chain A) in PDB entry 3MXW
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 TRP 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SO4 5.6 1.3 - - - -
47A PHE* 3.5 31.7 - + + +
48A ILE 3.5 8.5 - - - -
49A PRO* 3.5 16.8 + - + -
51A VAL 2.8 19.4 + - - -
52A ALA* 4.8 1.3 - - - -
53A GLU* 3.5 48.9 - - + +
58A ALA* 3.6 23.3 - - + -
59A SER* 3.5 15.5 - - - +
170A PHE* 3.3 0.4 - - - +
171A ASP* 1.3 76.8 - - - +
173A VAL* 1.3 65.4 + - - +
174A TYR* 3.5 39.9 - + + -
182A HIS* 3.7 21.3 - + - +
183A CYS* 3.4 3.1 - - - +
184A SER* 2.9 32.8 + - - +
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Residues in contact with VAL 173 (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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42A LEU* 4.1 5.7 - - + +
46A GLN 4.0 0.5 - - - +
47A PHE* 3.0 5.6 - - - +
48A ILE 2.9 32.9 + - - +
162A ALA* 3.5 26.9 - - + +
165A ALA* 3.9 7.2 - - + -
166A VAL* 3.8 33.7 - - + +
170A PHE* 3.7 23.8 - - + +
172A TRP* 1.3 80.1 - - - +
174A TYR* 1.3 63.7 + - - +
181A ILE* 3.6 24.2 - - + -
182A HIS 3.4 3.6 - - - -
183A CYS* 4.1 3.1 - - - -
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Residues in contact with TYR 174 (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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3A SO4 5.2 1.1 - - - -
45A LYS* 3.5 39.2 + - + +
46A GLN 3.5 9.9 - - - -
47A PHE* 3.9 16.6 - + + -
172A TRP* 3.5 38.1 - + + -
173A VAL* 1.3 77.3 - - - +
175A TYR* 1.3 61.5 + - - +
176A GLU* 2.9 49.1 + - + -
181A ILE* 3.5 4.6 - - - +
182A HIS* 2.8 42.8 + + + +
31L ASN* 3.8 23.0 + - - -
67L TYR* 6.1 0.3 - - - -
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Residues in contact with TYR 175 (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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42A LEU* 3.5 20.1 - - + +
43A ALA 3.4 29.6 - - - +
44A TYR* 3.7 25.8 - + + -
45A LYS* 3.0 23.6 + - - -
46A GLN 2.9 12.9 + - - +
155A ARG* 3.9 10.0 + - - +
158A TYR* 3.8 15.1 - - + +
159A GLY* 3.6 30.4 + - - -
162A ALA* 5.0 0.7 - - + -
173A VAL 4.4 0.2 - - - -
174A TYR* 1.3 68.9 - - - +
176A GLU* 1.3 58.7 + - - +
177A SER 3.2 23.6 - - - -
178A LYS* 4.5 8.6 + - - +
181A ILE* 3.4 24.9 - - + -
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Residues in contact with GLU 176 (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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3A SO4 2.8 25.5 + - - -
45A LYS* 2.8 29.3 + - - -
174A TYR* 2.9 47.3 + - + +
175A TYR* 1.3 72.5 - - - +
177A SER* 1.3 56.8 + - - +
180A HIS* 2.7 40.5 + - + +
182A HIS* 3.4 13.5 - - + +
400A ZN 3.6 8.3 - - - -
98H ARG* 3.9 2.1 + - - -
31L ASN* 6.0 1.3 - - - +
50L TYR* 3.9 26.0 - - + -
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Residues in contact with SER 177 (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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44A TYR* 3.4 14.6 - - - -
175A TYR* 3.2 13.7 - - - -
176A GLU* 1.3 78.5 - - - +
178A LYS* 1.3 64.8 + - - +
179A ALA 3.0 13.0 + - - -
180A HIS* 2.7 35.0 + - - +
98H ARG 3.1 29.6 + - - -
99H GLY* 4.4 1.6 - - - -
32L ASP* 5.5 1.3 - - - -
50L TYR* 3.5 11.9 - - - -
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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