Contacts of the strand formed by residues 136 - 145 (chain I) in PDB entry 4DKE
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 ALA 136 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I PRO* 4.8 9.4 - - + -
127I SER 5.8 2.2 - - - +
135I THR* 1.3 74.6 - - - +
137I ALA* 1.3 61.2 + - - +
138I LEU* 4.2 0.6 + - - -
182I VAL 4.0 0.3 - - - +
183I THR* 3.3 6.7 - - - -
184I VAL* 3.0 37.2 + - - +
186I SER* 4.2 17.0 - - - +
189I LEU* 4.6 19.7 - - + -
116M PHE* 4.7 6.1 - - - -
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Residues in contact with ALA 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I PRO* 3.8 12.5 - - - +
136I ALA* 1.3 76.5 - - - +
138I LEU* 1.3 61.8 + - - +
181I VAL* 5.1 0.7 - - + -
182I VAL 3.7 5.2 - - - +
183I THR* 4.4 11.2 - - + +
116M PHE* 3.5 45.7 - - + -
118M PHE* 3.3 24.7 - - + -
135M LEU* 4.4 8.5 - - + -
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Residues in contact with LEU 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 3.5 14.6 - - - +
126I PRO* 4.1 18.2 - - + -
136I ALA 6.3 0.4 - - - -
137I ALA* 1.3 74.8 - - - +
139I GLY* 1.3 61.3 + - - +
154I TRP* 3.6 22.2 - - + -
181I VAL* 3.5 6.3 - - - +
182I VAL* 2.9 57.0 + - + +
184I VAL* 4.5 9.9 - - + -
189I LEU* 4.8 9.0 - - + -
194I TYR* 3.6 35.4 - - + -
211I VAL* 4.0 15.7 - - + +
118M PHE* 4.3 4.9 - - - -
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Residues in contact with GLY 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I PRO 3.6 0.3 - - - -
124I LEU* 2.6 45.5 + - - +
138I LEU* 1.3 79.7 - - - +
140I CYS* 1.3 56.9 + - - -
154I TRP* 3.5 18.6 - - - -
180I SER 3.3 12.6 - - - -
181I VAL* 4.2 0.4 - - - -
211I VAL* 3.6 8.2 - - - +
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Residues in contact with CYS 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I VAL* 3.8 15.5 - - + -
122I PHE 3.3 4.5 - - - -
124I LEU* 3.7 3.8 - - - -
139I GLY* 1.3 78.4 - - - -
141I LEU* 1.3 61.2 + - - +
142I VAL* 3.8 6.4 + - + +
152I VAL* 5.7 0.7 - - + -
154I TRP* 3.9 6.3 - - + -
179I SER* 3.3 4.0 - - - -
180I SER* 3.1 33.3 + - - +
196I CYS* 2.0 52.9 - - + -
198I VAL* 5.5 0.2 - - + -
209I LYS* 4.3 4.7 - - - -
211I VAL* 4.2 12.8 - - - -
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Residues in contact with LEU 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I SER 3.5 0.7 - - - +
121I VAL* 3.1 7.4 - - - +
122I PHE* 2.7 51.7 + - + +
124I LEU* 3.9 15.8 - - + +
140I CYS* 1.3 72.2 - - - +
142I VAL* 1.3 73.5 + - - +
143I LYS* 3.5 29.6 - - + -
177I SER* 3.9 9.6 - - - +
178I LEU 3.8 8.5 - - - +
179I SER* 3.9 13.2 - - - +
124M GLN* 4.6 8.7 - - - +
131M SER* 3.6 33.4 - - - +
133M VAL* 4.3 15.7 - - + -
178M THR* 5.5 2.5 - - + -
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Residues in contact with VAL 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I PRO* 3.5 29.6 - - + -
120I SER 3.9 1.8 - - - -
121I VAL* 4.4 5.4 - - + +
140I CYS* 4.3 10.3 - - + +
141I LEU* 1.3 77.9 - - - +
143I LYS* 1.3 58.1 + - - +
145I TYR* 4.0 15.1 - - + -
150I VAL* 4.3 12.1 - - + -
152I VAL* 4.5 13.7 - - + -
177I SER* 3.4 3.8 + - - -
178I LEU* 2.8 47.8 + - + +
180I SER 5.3 1.1 - - - +
198I VAL* 3.9 26.9 - - + -
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Residues in contact with LYS 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119I PRO* 3.3 2.2 - - - +
120I SER* 2.9 42.7 + - - +
122I PHE* 4.6 11.4 - - + -
141I LEU* 3.5 19.7 - - + -
142I VAL* 1.3 76.0 - - - +
144I ASP* 1.3 104.1 + - - +
145I TYR* 3.7 1.8 - - - -
171I GLN* 3.4 20.6 - - - +
176I TYR 4.0 0.4 - - - -
177I SER* 4.1 7.4 - - - +
124M GLN* 4.6 5.4 - - - +
129M THR* 3.7 29.3 + - - +
131M SER* 3.9 22.6 + - - +
180M THR* 5.2 10.3 - - - +
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Residues in contact with ASP 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I LYS* 3.2 19.1 + - - +
118I GLY 3.1 17.3 - - - +
120I SER* 5.3 3.1 + - - +
122I PHE* 6.1 0.2 - - - -
143I LYS* 1.3 104.5 + - - +
145I TYR* 1.3 55.6 + - - +
171I GLN* 2.8 26.6 + - - +
173I SER* 4.2 6.6 + - - -
175I LEU* 3.5 29.4 - - + +
176I TYR 3.1 14.0 + - - -
129M THR* 5.4 0.7 - - - +
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Residues in contact with TYR 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I LYS* 4.0 7.2 - - - +
118I GLY 3.9 1.1 - - - -
119I PRO* 3.6 40.6 - - + -
142I VAL* 4.0 23.8 - - + -
144I ASP* 1.3 76.8 - - - +
146I PHE* 1.3 65.8 + - - +
147I PRO 3.5 19.3 - - - -
148I GLU* 3.4 23.8 + - + -
150I VAL* 3.7 24.2 - - + +
168I ALA* 3.5 8.8 - - - +
175I LEU* 3.8 3.6 - - - +
176I TYR* 2.8 56.9 + + + +
177I SER 4.3 0.7 - - - -
178I LEU* 3.2 26.6 - - + +
200I HIS* 4.2 2.5 - - + -
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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