Contacts of the strand formed by residues 176 - 185 (chain B) 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 GLU 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ASP* 5.0 4.5 - - - +
85A ARG* 2.4 53.6 + - - +
162B SER* 3.4 4.5 - - - -
163B LEU* 2.5 49.2 + - + +
174B THR 4.8 2.2 - - - +
175B PRO* 1.3 75.5 - - - +
177B LEU* 1.3 68.3 + - - +
178B LEU* 3.4 10.1 + - + +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG* 6.2 0.3 - - - +
195A PRO* 5.6 3.5 - - - +
196A SER* 2.9 31.5 + - - +
160B ARG* 3.5 50.0 - - + +
161B SER 4.0 0.7 - - - +
162B SER* 3.8 15.3 - - - +
175B PRO 4.2 1.4 + - - -
176B GLU* 1.3 76.3 - - - +
178B LEU* 1.3 69.7 + - - +
179B LEU 3.9 5.8 - - - +
180B GLU* 3.4 24.7 - - - +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ARG* 3.7 38.4 - - + +
195A PRO 3.5 16.8 - - - +
196A SER* 3.7 5.8 - - - -
135B LEU* 4.1 9.6 - - + -
161B SER* 3.1 15.0 + - - +
162B SER 4.4 1.8 - - - -
163B LEU* 3.6 25.6 - - + +
176B GLU* 3.6 23.3 - - + +
177B LEU* 1.3 75.4 - - - +
179B LEU* 1.3 74.6 + - + +
211B VAL* 4.0 25.4 - - + -
219B VAL* 4.0 19.5 - - + -
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 5.4 5.8 - - + +
195A PRO 4.9 1.1 - - - +
196A SER 4.0 1.1 - - - -
199A PHE* 3.4 39.9 - - + -
135B LEU* 4.2 16.2 - - + +
160B ARG* 3.0 7.1 - - - +
161B SER* 2.9 32.8 + - - +
177B LEU* 3.9 0.4 - - - +
178B LEU* 1.3 90.6 - - + +
180B GLU* 1.3 61.9 + - - +
207B PHE* 3.4 22.7 - - + -
208B GLY* 3.4 8.7 - - - +
209B GLY* 3.2 40.6 - - - +
211B VAL* 4.6 7.9 - - + -
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Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLN* 2.9 22.1 + - - +
114A VAL* 4.6 1.0 - - - +
196A SER* 3.2 26.6 + - - +
197A THR* 3.7 18.1 - - + +
158B THR* 5.2 5.9 - - - +
159B LEU 3.3 16.8 - - - +
160B ARG* 2.6 44.0 + - + +
177B LEU* 3.4 15.1 - - + +
179B LEU* 1.3 78.1 - - - +
181B GLY* 1.3 64.7 + - - +
182B ALA* 5.5 3.3 - - + +
207B PHE* 4.0 7.3 - - - -
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLN* 4.2 3.1 - - - -
114A VAL* 5.3 1.8 - - - -
166A SER* 3.6 14.1 - - - -
158B THR* 4.0 0.3 - - - -
159B LEU* 2.9 31.6 + - - +
180B GLU* 1.3 77.5 - - - +
182B ALA* 1.3 62.6 + - - +
205B VAL* 4.0 10.1 - - - -
207B PHE* 3.6 16.1 - - - -
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 5.3 2.9 - - + +
164A LEU* 3.6 21.3 - - + -
165A HIS* 3.7 5.7 + - - -
166A SER* 2.4 40.7 + - - +
157B VAL 3.6 4.0 - - - -
158B THR* 3.0 34.8 - - + +
180B GLU* 5.5 3.8 - - + +
181B GLY* 1.3 73.9 - - - -
183B GLU* 1.3 62.1 - - - +
205B VAL* 4.1 5.9 - - - +
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LYS* 4.8 0.2 + - - -
164A LEU 4.2 3.6 - - - +
165A HIS* 2.6 39.6 + - + +
166A SER* 5.4 2.9 + - - +
157B VAL* 2.8 44.5 + - + +
182B ALA* 1.3 74.1 - - - +
184B THR* 1.3 70.2 + - - +
185B VAL* 4.0 14.3 + - + +
203B THR* 3.6 23.9 + - + +
204B SER 4.1 5.0 - - - +
205B VAL* 3.9 23.0 - - + +
183D GLU* 3.5 16.5 - - - +
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Residues in contact with THR 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLU* 6.5 0.4 - - - -
162A PRO 4.0 13.7 - - - +
163A TRP* 3.1 10.5 - - - +
164A LEU* 2.6 52.3 + - + +
165A HIS* 5.2 4.2 - - - -
154B GLY* 5.7 2.0 - - - -
155B ARG 3.0 15.9 - - - +
156B SER* 3.3 24.5 - - - -
157B VAL 5.4 0.2 - - - +
158B THR* 5.9 1.1 - - + -
183B GLU* 1.3 79.6 - - - +
185B VAL* 1.3 64.8 + - - +
186B THR* 5.9 2.0 - - - -
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A HIS* 6.4 0.4 - - + -
143B GLY 5.6 5.6 - - - +
155B ARG* 2.7 41.8 + - + +
157B VAL* 6.3 1.1 - - + -
183B GLU* 4.0 22.2 + - + +
184B THR* 1.3 79.9 - - - +
186B THR* 1.3 60.0 + - - +
187B PRO* 3.8 25.4 - - + -
201B TRP* 5.7 5.4 - - + -
203B THR* 5.1 15.3 - - + +
183D GLU* 5.5 2.9 - - - +
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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