Contacts of the strand formed by residues 173 - 183 (chain B) in PDB entry 5T5W
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 HIS 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B LYS* 3.7 4.2 - - - +
145B GLU* 2.8 45.8 + - + +
171B SER 4.3 5.4 + - - -
172B GLU* 1.3 80.3 + - - +
174B HIS* 1.3 54.2 + - - +
175B CYS* 5.3 0.2 - - - -
197B CYS* 5.7 4.9 - - + -
198B PHE 3.3 14.8 - - - +
199B LEU* 3.5 28.7 - - + +
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Residues in contact with HIS 174 (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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142B PHE* 3.6 40.4 - + + -
143B TRP* 3.6 2.7 - - - -
144B LYS* 3.8 25.4 - - - +
172B GLU* 3.0 48.0 + - + +
173B HIS* 1.3 73.7 - - - +
175B CYS* 1.3 61.6 + - - +
197B CYS* 3.2 1.2 - - - -
198B PHE* 2.9 46.0 + - + +
200B LEU* 3.3 29.4 - - + +
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Residues in contact with CYS 175 (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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142B PHE* 3.8 5.4 - - - -
143B TRP* 2.8 57.3 + - + +
145B GLU* 3.9 25.4 - - - -
174B HIS* 1.3 75.1 - - - +
176B LEU* 1.3 62.6 + - - +
195B PRO* 4.0 4.5 - - + -
196B THR 3.2 4.9 - - - +
197B CYS* 2.0 47.3 - - - -
198B PHE* 4.7 0.2 - - - -
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Residues in contact with LEU 176 (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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110B LEU* 4.2 12.1 - - + +
112B LEU* 3.5 30.1 - - + -
119B LEU* 3.7 27.1 - - + -
121B ALA* 4.2 6.1 - - + -
140B VAL* 3.6 23.1 - - + -
141B ALA 3.3 15.9 - - - +
142B PHE* 3.5 26.2 - - + -
143B TRP* 4.1 1.6 - - - -
164B ILE* 4.0 5.4 - - + -
175B CYS* 1.3 73.9 - - - +
177B SER* 1.3 58.8 + - - +
193B SER* 4.9 0.3 + - - -
194B LYS 4.1 1.7 - - - +
195B PRO* 3.3 2.8 - - - +
196B THR* 2.8 38.6 + - - +
198B PHE* 3.7 11.7 - - + -
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Residues in contact with SER 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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110B LEU* 3.8 3.6 - - - +
140B VAL* 3.4 6.2 - - - +
141B ALA* 2.7 41.0 + - - +
143B TRP* 3.5 25.3 - - - -
176B LEU* 1.3 75.9 - - - +
178B ALA* 1.3 66.5 + - - +
192B PHE* 3.2 19.0 - - - +
193B SER* 3.0 28.7 + - - -
195B PRO* 4.5 2.9 - - - +
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Residues in contact with ALA 178 (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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107B PRO* 4.0 0.2 - - - +
108B PRO* 3.6 28.4 - - + +
110B LEU* 3.7 25.4 - - + -
138B TYR* 4.3 4.0 - - + -
139B GLU 3.2 11.4 - - - +
140B VAL* 4.1 6.5 - - + -
177B SER* 1.3 80.8 + - - +
179B ARG* 1.3 59.9 + - - +
192B PHE* 3.5 5.0 - - - -
193B SER* 3.0 30.2 + - - +
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Residues in contact with ARG 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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141A GLU* 5.9 0.4 + - - -
108B PRO* 3.9 5.2 - - - -
138B TYR* 3.0 5.2 - - - -
139B GLU* 2.9 65.0 + - + +
152B LEU* 5.8 2.4 - - - +
178B ALA* 1.3 74.2 - - - +
180B THR* 1.3 64.1 + - - +
181B ILE* 4.3 1.5 - - + +
189B TYR* 3.4 43.0 - - - +
190B SER 3.6 14.3 + - - +
191B LYS 3.4 22.9 - - - +
192B PHE* 3.5 35.7 - - + -
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Residues in contact with THR 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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17B PHE* 4.4 0.9 - - + -
105B PRO* 4.0 18.7 - - + +
106B ALA 2.6 27.0 + - - -
108B PRO* 3.2 5.1 - - - +
125B TYR* 2.5 36.5 + - + +
136B LEU* 4.4 15.7 - - + -
137B LYS 3.3 7.2 - - - +
179B ARG* 1.3 73.6 - - - +
181B ILE* 1.3 70.2 + - - +
182B TYR 4.0 0.2 - - - -
188B LYS 3.8 0.9 - - - +
189B TYR* 3.7 3.1 - - - +
190B SER* 3.2 33.6 + - - -
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Residues in contact with ILE 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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141A GLU* 5.4 0.2 - - - +
142A THR* 3.6 20.9 - - + -
135B ASP 3.7 2.1 - - - +
137B LYS* 2.4 51.0 + - - +
139B GLU* 4.3 18.4 - - + +
155B VAL* 3.8 35.9 - - + -
179B ARG* 4.3 7.2 - - - +
180B THR* 1.3 74.5 - - - +
182B TYR* 1.3 60.7 + - - +
183B THR* 3.9 3.1 + - - +
187B PRO* 4.1 13.9 - - + -
188B LYS 3.6 5.4 - - - +
189B TYR* 3.7 44.0 - - + +
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Residues in contact with TYR 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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17B PHE* 5.3 0.7 - + + -
100B LEU* 2.8 42.6 + - - +
101B PHE* 5.5 1.8 - - - -
103B VAL* 3.6 30.1 - - + -
105B PRO* 4.3 15.2 - - + +
134B LEU* 3.7 39.9 - - + -
135B ASP 3.5 13.5 - - - -
136B LEU* 4.1 11.0 - - + -
180B THR* 4.0 1.6 - - - +
181B ILE* 1.3 71.2 - - - +
183B THR* 1.3 67.4 + - - +
184B PHE* 3.1 29.5 - + + +
186B VAL 3.6 3.3 - - - +
187B PRO* 3.3 0.9 - - - +
188B LYS* 2.7 53.7 + - + +
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Residues in contact with THR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 5.6 0.2 - - + -
142A THR* 2.6 45.0 + - - +
143A TRP* 5.5 1.8 - - + -
135B ASP* 3.3 33.4 + - - +
181B ILE* 4.1 1.6 + - - +
182B TYR* 1.3 82.7 + - - +
184B PHE* 1.3 63.2 + - - +
186B VAL 4.1 2.7 - - - -
187B PRO* 3.8 20.5 - - + +
14C PRO* 3.8 28.3 - - + -
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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