Contacts of the strand formed by residues 173 - 182 (chain X) in PDB entry 4MXV
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 TYR 173 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12X SER* 5.2 0.3 + - - -
103X LYS* 5.8 4.3 - - - -
105X GLU* 3.4 30.0 + - - +
138X ASN* 3.1 4.3 + - - -
139X PHE* 2.9 56.2 + - + +
140X TYR* 3.9 20.1 - + - -
141X PRO 4.1 0.4 - - - -
142X ARG* 3.6 52.6 - - + +
163X VAL* 4.1 5.6 - - + -
164X THR* 3.5 24.5 - - - -
165X GLU* 4.4 1.1 - - - -
166X GLN* 3.4 41.9 + - + +
172X THR* 1.3 75.7 + - - +
174X SER* 1.3 69.3 + - - +
164Y HIS* 5.8 0.9 - - - -
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Residues in contact with SER 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X LEU 3.3 11.0 - - - -
137X ASN* 3.0 14.8 + - - -
138X ASN* 3.0 20.4 + - - -
139X PHE* 3.7 3.4 - - - -
163X VAL* 3.5 3.6 - - - +
164X THR* 3.1 30.1 + - - -
173X TYR* 1.3 81.0 + - - +
175X LEU* 1.3 59.7 + - - +
164Y HIS* 3.5 13.8 + - - -
166Y PHE* 3.0 27.1 - - - -
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Residues in contact with LEU 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X LEU* 3.5 3.5 - - - +
136X LEU* 2.6 49.5 + - + +
139X PHE* 3.5 18.0 - - + -
142X ARG 5.6 1.8 - - - +
144X ALA* 4.5 23.3 - - + +
146X VAL* 4.0 24.5 - - + -
161X GLU* 3.7 23.6 - - - +
162X SER 3.6 4.0 - - - +
163X VAL* 3.7 23.6 - - + -
174X SER* 1.3 73.9 - - - +
176X SER* 1.3 78.2 + - - +
177X SER* 4.0 6.7 - - - +
166Y PHE* 3.6 3.1 - - - -
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Residues in contact with SER 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X VAL* 4.1 9.1 - - - +
134X CYS 3.6 4.3 - - - -
135X LEU* 4.7 2.2 - - - +
161X GLU* 3.2 3.6 - - - -
162X SER* 3.0 35.6 + - - -
175X LEU* 1.3 77.7 - - - +
177X SER* 1.3 62.3 + - - +
178X THR* 4.1 11.0 + - - -
166Y PHE* 3.3 39.3 - - - -
179Y SER* 3.1 15.3 + - - -
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Residues in contact with SER 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X VAL* 3.3 3.5 - - - +
134X CYS* 2.8 41.4 + - - +
146X VAL* 4.1 14.8 - - - +
148X TRP* 2.9 27.6 + - - -
159X SER* 4.4 4.2 - - - -
160X GLN 3.3 8.0 + - - -
161X GLU* 3.9 17.2 + - - +
175X LEU* 4.0 8.1 - - - -
176X SER* 1.3 76.2 + - - +
178X THR* 1.3 63.0 + - - +
179X LEU 4.0 0.2 - - - -
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Residues in contact with THR 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131X SER* 4.0 17.5 - - - +
132X VAL 3.4 4.3 - - - +
133X VAL* 3.7 25.3 - - + +
148X TRP* 4.5 0.7 - - - -
158X ASN 3.7 0.5 - - - +
159X SER* 3.5 3.9 - - - -
160X GLN* 2.8 37.7 + - - +
176X SER* 4.1 8.7 + - - -
177X SER* 1.3 76.8 + - - +
179X LEU* 1.3 71.8 + - - +
180X THR* 3.6 9.5 + - - +
141Y LEU* 4.9 10.0 - - + +
169Y VAL* 5.9 3.6 - - - +
177Y SER* 5.9 1.8 - - - +
179Y SER* 5.4 1.0 + - - -
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Residues in contact with LEU 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X ALA 3.8 0.4 - - - +
131X SER* 3.4 2.8 - - - -
132X VAL* 2.7 51.3 + - + +
148X TRP* 3.7 51.6 - - + +
150X VAL* 4.0 17.5 - - + -
155X GLN* 4.0 7.9 - - + -
158X ASN* 3.4 42.0 - - - +
159X SER* 4.5 0.7 - - - +
178X THR* 1.3 72.8 - - - +
180X THR* 1.3 60.2 + - - +
181X LEU* 3.6 24.0 - - + -
192X TYR* 4.5 7.0 - - + -
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Residues in contact with THR 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129X THR* 5.7 3.6 - - - +
130X ALA 3.5 4.2 + - - -
131X SER* 3.7 16.3 + - - -
158X ASN* 3.1 33.4 + - + +
159X SER* 5.4 0.7 - - - -
160X GLN* 5.6 7.2 - - + +
178X THR* 4.1 11.0 - - - +
179X LEU* 1.3 80.0 - - - +
181X LEU* 1.3 64.2 + - - +
143Y LYS* 4.3 13.6 + - - -
171Y GLN* 5.3 5.6 + - + +
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Residues in contact with LEU 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129X THR* 5.0 3.6 - - - +
130X ALA* 2.9 38.3 + - + +
132X VAL* 5.6 2.2 - - + -
150X VAL* 4.6 7.4 - - + -
155X GLN* 5.1 1.8 - - - +
158X ASN* 4.8 9.6 - - - +
179X LEU* 3.6 38.4 - - + -
180X THR* 1.3 75.8 + - - +
182X SER* 1.3 77.7 + - - +
185X ASP* 4.1 11.9 - - + +
186X TYR* 3.7 34.5 - - + +
192X TYR* 4.5 10.1 - - + +
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Residues in contact with SER 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X GLY 3.8 8.7 - - - -
129X THR* 4.4 7.4 - - - +
181X LEU* 1.3 80.1 - - - +
183X LYS* 1.3 59.9 + - - +
184X ALA* 3.4 12.0 - - - +
185X ASP* 3.0 31.4 + - - +
186X TYR* 3.0 25.6 + - - +
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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