Contacts of the strand formed by residues 141 - 148 (chain D) in PDB entry 1DGB
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 GLY 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ALA 3.3 9.4 - - - -
32A GLY* 3.3 18.6 + - - -
33A ASN* 3.5 1.2 + - - -
138D THR* 2.5 40.8 + - - +
139D GLU 3.2 3.4 + - - -
140D ASP* 1.3 79.1 - - - +
142D ASN* 1.3 68.6 + - - -
340D PRO* 4.6 2.1 - - - +
378D PRO* 4.5 0.9 - - - -
381D ALA* 3.7 5.9 - - - +
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Residues in contact with ASN 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 2.9 14.9 + - + +
33A ASN* 3.2 18.4 + - - +
135D LYS* 4.2 15.9 - - + +
136D PHE 3.2 6.1 - - - +
137D TYR* 3.2 38.9 - - - -
138D THR 4.1 0.5 + - - +
141D GLY* 1.3 71.4 - - - -
143D TRP* 1.3 60.4 + - - +
144D ASP* 4.1 4.7 - - - +
338D ASN* 3.5 22.9 - - - +
340D PRO* 4.3 0.6 - - - +
371D LEU* 6.0 0.8 - - - +
376D ASN 3.4 24.4 + - - -
377D CYS 3.8 1.8 - - - -
378D PRO* 3.4 25.6 - - - +
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Residues in contact with TRP 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 5.8 0.2 - + - -
99D VAL* 4.4 10.3 - - + -
100D PHE* 4.2 19.3 - + - -
136D PHE* 2.8 92.9 + + + +
138D THR* 4.5 4.0 - - + -
142D ASN* 1.3 74.0 - - - +
144D ASP* 1.3 70.6 + - - +
145D LEU* 4.2 18.9 - - + +
220D PHE* 6.1 1.8 - - - -
234D PHE* 3.9 30.9 - + - -
279D PHE* 4.2 11.0 - + - -
338D ASN 3.2 17.5 - - - -
339D MET* 4.1 6.6 - - + +
340D PRO* 3.6 25.1 - - + -
343D ILE* 3.4 34.7 - - + +
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Residues in contact with ASP 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL 3.5 2.0 - - - +
135D LYS* 2.6 48.4 + - - +
142D ASN* 4.7 0.6 - - - +
143D TRP* 1.3 81.3 + - - +
145D LEU* 1.3 60.3 + - - +
146D VAL* 3.4 6.7 + - + +
333D ALA 3.9 0.3 - - - +
334D PHE* 3.4 12.2 - - + -
335D ASP 2.7 40.1 + - - +
336D PRO* 4.0 8.7 - - - +
338D ASN* 2.7 35.4 + - - +
339D MET* 5.4 0.5 - - - +
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Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PHE 3.9 1.0 - - - +
134D VAL* 2.8 40.0 + - + +
136D PHE* 3.9 18.8 - - + -
143D TRP* 3.7 18.6 + - + +
144D ASP* 1.3 68.9 - - - +
146D VAL* 1.3 59.2 + - - +
147D GLY 3.3 4.7 + - - -
216D GLY* 4.0 17.0 - - - -
220D PHE* 4.6 10.5 - - + -
234D PHE* 3.9 31.2 - - + -
236D TYR* 3.9 22.7 - - + +
279D PHE* 3.8 34.5 - - + -
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Residues in contact with VAL 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ALA* 4.1 11.0 - - + -
144D ASP 3.4 11.1 + - - +
145D LEU* 1.3 74.0 - - - +
147D GLY* 1.3 57.1 + - - +
216D GLY 4.8 2.0 - - - +
334D PHE* 3.7 24.5 - - + +
336D PRO* 3.7 27.3 - - + +
354D ARG* 3.0 31.9 + - - +
358D TYR* 4.1 8.1 - - + -
1203D HEM 3.2 49.4 - - + +
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Residues in contact with GLY 147 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D PHE* 2.7 46.1 + - - -
145D LEU 3.3 3.8 + - - -
146D VAL* 1.3 74.6 - - - +
148D ASN* 1.3 65.2 + - - +
215D TYR 3.1 17.5 - - - -
216D GLY* 4.6 1.8 - - - -
236D TYR* 3.6 5.6 + - - -
1203D HEM 3.1 11.2 - - - +
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Residues in contact with ASN 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D HIS* 3.9 7.5 + - - -
129D PRO* 5.1 7.5 - - - +
130D ARG 3.2 8.7 - - - +
131D GLY* 3.6 11.1 - - - -
132D PHE* 4.1 4.7 - - - +
147D GLY* 1.3 79.8 - - - +
149D ASN* 1.3 59.9 + - - +
150D THR* 2.9 30.4 + - + +
152D ILE 5.1 0.6 + - - -
153D PHE* 4.0 21.6 - - - -
213D ASN 4.4 0.9 - - - -
214D GLY 3.6 0.3 - - - -
215D TYR* 2.8 30.4 + - - +
217D SER* 4.9 0.2 + - - -
1203D HEM 3.3 44.2 - - + +
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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