Contacts of the strand formed by residues 151 - 157 (chain D) in PDB entry 3COG
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 THR 151 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D GLN* 2.3 35.7 + - - +
108D ILE* 3.9 21.5 - - + +
147D ILE* 3.7 8.9 - - + -
148D THR* 2.9 27.9 + - - +
149D PRO 4.3 3.1 - - - +
150D GLU* 1.3 74.9 - - - +
152D LYS* 1.3 70.1 + - - +
153D LEU 4.1 6.7 - - - +
154D VAL* 4.1 9.2 - - + -
181D ASP 5.5 0.2 + - - -
182D ILE* 3.4 38.7 - - + +
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Residues in contact with LYS 152 (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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101D LEU* 3.7 19.1 - - + -
105D ASP* 3.6 33.8 + - + +
106D GLN 3.1 5.5 + - - +
149D PRO 4.7 8.7 + - - -
150D GLU* 3.9 9.4 - - - +
151D THR* 1.3 83.3 - - - +
153D LEU* 1.3 62.2 + - - +
181D ASP* 3.3 37.4 - - - +
182D ILE* 3.5 7.9 - - - -
183D ILE* 2.9 32.1 + - + +
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Residues in contact with LEU 153 (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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97D ILE* 4.4 11.7 - - + +
98D THR* 4.4 15.9 - - - +
101D LEU* 3.8 27.6 - - + -
106D GLN 3.6 2.3 + - - +
107D ILE* 3.5 26.8 - - + -
108D ILE 2.9 24.3 + - - -
121D PHE* 4.7 1.1 - - + -
151D THR* 4.1 2.0 - - - +
152D LYS* 1.3 81.3 - - - +
154D VAL* 1.3 75.6 + - - +
155D TRP* 4.4 14.6 - - + +
183D ILE* 3.4 22.7 - - + +
185D VAL* 3.7 27.4 - - + -
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Residues in contact with VAL 154 (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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108D ILE* 3.2 17.9 - - + +
137D CYS* 4.8 0.7 - - - -
143D LEU* 4.1 25.1 - - + -
147D ILE* 5.1 2.2 - - + -
151D THR* 4.1 11.4 - - + -
153D LEU* 1.3 80.9 - - - +
155D TRP* 1.3 59.2 + - - +
156D ILE* 4.1 14.1 - - + -
176D VAL* 3.9 24.5 - - + -
182D ILE* 4.0 12.3 - - + -
183D ILE 2.8 12.0 + - - +
184D LEU* 3.6 17.6 - - + +
185D VAL* 2.9 29.6 + - - +
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Residues in contact with TRP 155 (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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94D THR* 3.3 42.2 - - + -
97D ILE* 3.7 34.3 - - + -
107D ILE* 4.9 0.9 - - + -
108D ILE 2.7 13.5 + - - +
109D CYS* 4.0 8.1 - - - -
110D MET* 2.8 27.9 + - - +
113D VAL* 4.5 4.5 - - + -
117D THR* 3.6 26.9 + - + +
121D PHE* 3.8 26.7 - + + -
153D LEU* 4.4 12.1 - - + -
154D VAL* 1.3 71.3 - - - +
156D ILE* 1.3 68.8 + - - +
157D GLU* 4.8 3.4 - - - +
185D VAL* 3.7 31.9 - - + -
187D ASP* 4.2 18.3 + - + +
207D MET* 3.9 20.2 - - + -
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Residues in contact with ILE 156 (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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110D MET* 3.9 7.2 - - + -
137D CYS* 4.2 25.8 - - + -
154D VAL* 4.1 20.0 - - + -
155D TRP* 1.3 84.5 - - - +
157D GLU* 1.3 56.7 + - - +
158D THR* 4.0 17.7 - - + -
167D ILE* 3.7 28.5 - - + -
169D ILE* 4.3 5.8 - - + -
172D CYS* 5.4 3.8 - - + -
184D LEU* 4.2 9.6 - - + -
185D VAL 2.9 18.7 + - - +
186D VAL* 3.4 22.0 - - + -
187D ASP* 2.8 33.3 + - - +
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Residues in contact with GLU 157 (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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110D MET* 4.2 5.8 - - - +
113D VAL* 3.3 19.7 - - + +
114D TYR* 2.7 34.8 + - - +
117D THR* 4.3 2.6 + - - -
155D TRP* 4.8 2.3 + - - +
156D ILE* 1.3 74.1 - - - +
158D THR* 1.3 63.9 + - - +
159D PRO 4.1 4.3 - - - +
160D THR* 3.3 28.4 - - + +
161D ASN* 2.9 33.6 + - - +
167D ILE* 3.6 9.4 - - - +
187D ASP* 3.7 31.2 - - + +
500D PLP 3.8 12.3 - - + +
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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