Contacts of the strand formed by residues 118 - 126 (chain B) in PDB entry 3DPR
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 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B ALA* 4.1 17.0 - - + +
115B SER* 3.0 52.4 + - - +
117B PHE* 1.3 80.0 - - + +
119B GLN* 1.3 61.8 + - - +
194B LEU* 4.6 9.9 - - + -
195B ARG 4.7 6.2 + - - -
231B LEU* 4.6 9.4 - - + -
232B GLU 3.8 8.3 - - - +
233B THR* 3.2 23.3 - - + +
235B SER* 3.7 15.9 + - - -
237B ILE* 3.6 22.9 + - - +
240B ILE* 5.3 6.2 - - + +
122C THR* 2.9 22.2 + - - -
123C ALA 4.1 1.9 + - - -
203C PRO* 5.6 1.1 - - - -
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Residues in contact with GLN 119 (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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118B HIS* 1.3 72.0 - - - +
120B GLY* 1.3 58.5 + - - +
194B LEU* 3.4 11.8 - - - +
195B ARG 5.3 0.4 - - - +
230B PRO 3.5 1.3 + - - +
231B LEU* 3.5 4.0 - - - +
232B GLU* 3.1 66.1 + - + +
120C CYS 3.2 19.0 + - - +
121C GLY* 3.5 7.5 - - - +
122C THR* 3.3 23.2 + - - +
125C THR* 5.1 1.2 + - - +
203C PRO* 3.3 24.0 - - + +
205C THR 3.0 30.1 + - - +
206C ALA* 4.1 6.7 - - - +
207C ARG* 4.4 7.7 - - - +
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Residues in contact with GLY 120 (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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71B TRP* 3.9 5.4 - - - -
119B GLN* 1.3 78.7 - - - +
121B THR* 1.4 64.5 + - - -
193B ASN* 3.0 17.5 + - - -
194B LEU* 3.3 25.8 - - - +
229B CYS* 3.1 16.2 - - - -
230B PRO 3.8 4.0 - - - -
120C CYS* 3.6 6.6 + - - -
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Residues in contact with THR 121 (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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71B TRP* 3.8 1.8 - - - -
120B GLY* 1.4 76.6 + - - -
122B LEU* 1.3 66.7 + - - +
191B PHE* 4.3 10.3 - - + -
192B ILE 3.3 12.3 - - - +
193B ASN* 3.2 12.1 + - + -
227B PRO* 3.4 5.2 - - - +
228B ILE* 2.9 44.7 + - + +
229B CYS* 2.7 20.5 + - - +
118C MET* 3.9 25.8 - - + -
120C CYS* 3.1 24.1 - - - +
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Residues in contact with LEU 122 (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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71B TRP* 3.7 36.6 - - + -
78B TRP* 4.7 1.8 - - + -
110B VAL* 6.1 1.8 - - + -
112B CYS* 5.0 1.8 - - + -
121B THR* 1.3 76.7 - - - +
123B ILE* 1.3 62.9 + - - +
124B VAL* 3.6 3.7 + - + +
191B PHE* 3.2 9.7 - - - -
192B ILE* 2.8 49.7 + - + +
225B ILE* 3.8 22.2 - - + -
226B ILE 3.3 1.6 - - - -
227B PRO* 3.2 45.1 - - + -
242B ILE* 4.0 22.4 - - + -
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Residues in contact with ILE 123 (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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122B LEU* 1.3 71.7 - - - +
124B VAL* 1.3 68.8 + - - +
125B ALA* 4.5 11.0 - - + -
181B LEU* 3.9 25.6 - - + -
184B ILE* 4.6 18.8 - - + -
185B THR* 5.9 0.2 - - + -
189B HIS* 5.0 5.2 - - + -
190B GLN 3.8 4.0 - - - +
191B PHE* 3.3 33.0 - - + -
224B VAL* 3.1 15.7 - - + +
225B ILE* 3.2 13.9 - - - -
226B ILE* 3.0 21.0 + - + +
228B ILE* 3.7 32.1 - - + -
52C LEU* 5.3 4.3 - - + -
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Residues in contact with VAL 124 (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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108B ILE* 6.0 0.9 - - + -
110B VAL* 3.8 30.5 - - + -
122B LEU* 4.0 6.3 - - + +
123B ILE* 1.3 76.5 - - - +
125B ALA* 1.3 59.2 + - - +
189B HIS* 3.0 4.1 - - - +
190B GLN 2.7 46.7 + - - +
192B ILE* 3.9 28.3 - - + -
200B ALA* 4.3 10.3 - - + -
202B ILE* 4.6 8.2 - - + +
223B LEU* 3.7 19.7 - - + -
224B VAL 3.7 0.7 - - - -
225B ILE* 4.0 11.2 - - + -
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Residues in contact with ALA 125 (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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123B ILE* 4.5 5.2 - - + -
124B VAL* 1.3 76.5 - - - +
126B LEU* 1.3 59.5 + - - +
127B ILE* 3.3 18.8 - - + +
184B ILE* 4.1 21.8 - - + -
187B PHE* 4.9 2.0 - - + -
188B PRO 3.3 9.9 - - - +
189B HIS* 4.0 9.4 - - + -
202B ILE* 5.2 0.9 - - - -
223B LEU* 3.2 4.2 - - - +
224B VAL* 2.7 42.9 + - + +
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Residues in contact with LEU 126 (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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34B ALA* 5.8 0.2 - - + -
82B LEU* 4.9 5.2 - - + -
106B TYR* 5.8 0.4 - - + -
108B ILE* 4.2 24.9 - - + -
125B ALA* 1.3 71.5 - - - +
127B ILE* 1.3 73.9 + - - +
128B PRO* 3.8 0.7 - - - +
187B PHE* 3.7 1.6 - - - +
188B PRO* 2.9 38.7 + - + +
202B ILE* 4.4 14.9 - - + +
204B ALA* 3.9 20.9 - - + -
221B TRP* 2.9 47.5 - - + -
222B SER 3.4 23.3 - - - +
223B LEU* 3.8 10.5 - - + +
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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