Contacts of the strand formed by residues 175 - 183 (chain K) in PDB entry 3QUM
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 175 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110K THR* 5.7 5.8 - - + +
143K LYS 3.8 2.9 - - - +
145K TYR* 3.1 55.3 + - + +
146K PHE* 4.6 16.1 - + - -
147K PRO 4.2 4.7 - - - -
148K GLU* 3.7 52.7 + - + +
168K ALA* 4.1 15.5 - - + -
169K VAL 4.0 2.2 - - - -
170K LEU* 3.3 50.0 - - + +
173K ASP 4.3 0.2 - - - -
174K LEU* 1.3 75.0 - - - +
176K THR* 1.3 59.9 + - - +
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Residues in contact with THR 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K LEU* 4.3 11.2 - - + -
142K VAL 3.6 15.0 - - - +
143K LYS* 3.0 50.0 + - - +
145K TYR* 4.6 0.7 - - - -
168K ALA* 3.1 6.1 - - - -
169K VAL* 2.9 43.8 + - + +
171K GLN* 6.1 0.3 - - - +
174K LEU 3.6 5.7 + - - -
175K TYR* 1.3 71.7 - - - +
177K LEU* 1.3 64.6 + - - +
160M LEU* 6.4 1.3 - - - -
178M THR* 5.2 6.1 - - + -
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Residues in contact with LEU 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K LEU* 3.8 3.5 - - - +
142K VAL* 3.1 39.8 + - + +
145K TYR* 4.0 21.1 - - + +
148K GLU* 5.8 0.2 - - - +
150K VAL* 3.7 35.4 - - + +
152K LEU* 5.6 4.3 - - + -
165K THR* 4.1 12.1 - - + -
166K PHE 2.9 31.2 - - - +
167K PRO* 4.0 12.6 - - + -
168K ALA* 4.3 2.9 - - + +
176K THR* 1.3 84.1 - - - +
178K SER* 1.3 67.5 + - - +
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Residues in contact with SER 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K LEU* 5.0 1.2 - - - +
140K CYS 3.7 8.7 + - - -
141K LEU* 4.4 11.7 - - - +
142K VAL* 6.0 0.4 - - - -
152K LEU* 5.8 0.2 - - - -
165K THR* 3.6 7.6 - - - +
166K PHE* 3.4 37.6 + - - +
167K PRO 4.9 1.8 + - - -
177K LEU* 1.3 79.6 - - - +
179K SER* 1.3 72.4 + - - +
133M VAL* 4.4 6.3 - - - +
135M PHE* 3.2 26.9 - - - -
176M SER* 4.4 9.9 - - - -
178M THR* 5.6 2.7 - - - -
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Residues in contact with SER 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K GLY* 3.0 3.6 - - - -
140K CYS* 2.8 39.1 + - - +
152K LEU* 3.3 35.8 - - - +
154K TRP* 3.1 23.8 + - - -
164K HIS 2.6 21.7 + - - -
165K THR* 3.8 2.0 + - - -
166K PHE* 4.5 1.6 - - - -
178K SER* 1.3 79.4 + - - +
180K SER* 1.3 58.4 + - - +
135M PHE* 4.0 5.3 - - - -
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Residues in contact with SER 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137K THR* 4.5 5.6 + - - -
138K LEU 3.1 9.0 - - - -
154K TRP* 4.4 0.9 - - - -
162K GLY 4.5 1.7 + - - -
163K VAL* 3.6 1.0 - - - +
164K HIS* 2.6 46.8 + - - +
166K PHE* 4.2 4.0 - - - -
179K SER* 1.3 77.4 + - - +
181K VAL* 1.3 60.1 + - - +
182K THR* 5.1 1.7 - - - +
135M PHE* 3.3 35.2 - - - -
137M ASN* 3.7 20.1 + - - -
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Residues in contact with VAL 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137K THR* 3.6 1.4 + - - -
138K LEU* 2.8 32.6 + - + +
154K TRP* 3.6 44.2 - - + +
159K LEU* 3.7 29.8 - - + -
162K GLY 3.4 9.9 - - - +
163K VAL* 3.7 19.1 - - + +
180K SER* 1.3 75.2 - - - +
182K THR* 1.3 69.3 + - - +
183K VAL* 4.1 2.5 - - + -
193K ILE* 3.7 16.6 - - + -
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Residues in contact with THR 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K SER* 4.3 14.1 + - - -
136K VAL 3.3 11.2 + - - -
137K THR* 3.5 21.8 - - - +
161K SER 4.3 3.1 - - - +
162K GLY* 3.2 31.8 + - - +
164K HIS* 6.1 1.3 - - - +
180K SER* 5.1 3.4 - - - +
181K VAL* 1.3 80.1 - - - +
183K VAL* 1.3 73.8 + - - +
137M ASN* 5.5 6.7 - - - +
138M ASN* 6.1 0.9 - - - +
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Residues in contact with VAL 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K SER 4.3 1.1 - - - -
135K SER* 3.6 4.4 + - - -
136K VAL* 3.1 39.1 + - + +
138K LEU* 4.8 3.1 - - + -
159K LEU* 3.4 34.8 - - + -
181K VAL* 4.1 4.5 - - + -
182K THR* 1.3 92.8 + - - +
184K THR* 1.3 71.7 + - - +
185K SER 3.1 0.2 + - - -
187K THR* 4.5 9.9 - - - +
188K TRP* 4.8 9.2 - - + -
193K ILE* 4.8 16.2 - - + -
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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