Contacts of the strand formed by residues 163 - 171 (chain B) in PDB entry 4LT6
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 ILE 163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B GLU* 6.1 0.2 - - - +
56B GLU 5.6 0.4 - - - +
59B HIS* 3.7 30.1 - - + -
60B ARG* 4.1 34.5 - - + +
63B VAL* 3.9 20.0 - - + -
113B ILE* 3.6 31.4 - - + -
159B GLU* 4.3 1.1 - - - -
160B PHE* 2.7 35.8 + - - +
162B GLY* 1.3 80.0 - - - +
164B GLU* 1.3 70.5 + - - +
165B ILE* 3.6 10.1 + - + +
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Residues in contact with GLU 164 (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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110B GLY 4.7 8.3 - - - +
111B ALA 5.1 2.9 + - - +
112B ASP* 3.3 33.4 - - + +
113B ILE 2.9 24.8 + - - -
146B ARG* 5.8 5.5 + - - +
158B PHE 3.6 9.0 - - - +
159B GLU* 4.4 11.7 - - + +
162B GLY 3.6 4.2 + - - +
163B ILE* 1.3 74.1 - - - +
165B ILE* 1.3 63.9 + - - +
166B ASP* 5.1 5.8 - - - +
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 3.9 26.7 - - + -
64B LEU* 4.9 7.9 - - + -
67B LEU* 4.3 17.9 - - + -
113B ILE* 3.6 14.6 - - + +
115B ALA* 4.2 14.8 - - + -
156B ILE 3.7 1.6 - - - +
157B LYS* 3.5 1.9 - - - +
158B PHE* 2.8 71.3 + - + +
160B PHE* 4.1 3.6 - - + -
163B ILE* 3.8 13.7 - - + +
164B GLU* 1.3 79.4 - - - +
166B ASP* 1.3 77.5 + - - +
167B LEU* 3.8 4.5 - - + +
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Residues in contact with ASP 166 (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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99B PHE* 5.1 1.4 - - - -
112B ASP* 4.0 21.7 - - - +
113B ILE 3.1 7.8 + - - +
114B ASP* 3.8 20.5 - - - +
115B ALA 3.0 27.0 + - - +
155B VAL* 3.8 14.8 - - + -
156B ILE 4.0 0.9 - - - -
157B LYS* 3.3 37.9 + - - +
164B GLU* 5.1 5.9 - - - +
165B ILE* 1.3 79.2 + - - +
167B LEU* 1.3 59.1 + - - +
168B VAL* 3.9 2.9 + - + +
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Residues in contact with LEU 167 (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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67B LEU* 4.0 9.9 - - + -
96B ILE* 4.0 22.2 - - + -
115B ALA* 3.4 24.5 - - + +
117B CYS* 4.2 8.7 - - + +
128B PHE* 3.9 21.2 - - + -
132B PHE* 3.6 32.1 - - + -
136B LEU* 4.5 2.0 - - + -
155B VAL* 3.2 5.9 - - - +
156B ILE* 2.9 43.2 + - + +
158B PHE* 3.9 23.8 - - + -
165B ILE* 4.3 2.2 - - + -
166B ASP* 1.3 72.0 - - - +
168B VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 168 (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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99B PHE* 4.9 14.8 - - + -
115B ALA 2.7 16.1 + - - +
116B LEU* 3.2 9.6 - - + +
117B CYS* 2.6 33.6 + - - +
128B PHE* 4.4 3.1 - - - -
153B VAL* 3.8 16.8 - - + +
154B PRO 3.2 19.5 - - - +
155B VAL* 3.8 13.5 - - + -
166B ASP* 4.8 2.9 - - + +
167B LEU* 1.3 78.7 - - - +
169B PHE* 1.3 58.4 + - - +
199B SER* 3.3 40.2 - - - +
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Residues in contact with PHE 169 (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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74B TRP* 4.1 14.1 - + - -
116B LEU* 4.0 0.4 - - - -
117B CYS* 3.5 11.4 - - - -
119B ALA* 3.4 31.6 - - + -
123B VAL* 4.0 17.0 - - + -
124B GLU 4.1 1.8 - - - -
125B ARG* 2.7 74.1 + - + +
128B PHE* 3.4 44.7 - + + -
129B PHE* 5.2 0.2 - - + -
154B PRO 4.3 2.6 + - - -
168B VAL* 1.3 76.8 - - - +
170B ALA* 1.3 91.1 + - - +
171B ARG* 3.7 6.1 - - + -
199B SER* 3.0 12.7 + - - -
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Residues in contact with ALA 170 (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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116B LEU* 3.9 10.5 - - + -
117B CYS 3.1 6.9 + - - +
118B VAL* 3.6 6.9 - - + +
119B ALA 3.0 26.0 + - - -
169B PHE* 1.3 88.2 - - - +
171B ARG* 1.3 63.5 + - - +
172B LEU* 6.0 0.9 - - + -
196B CYS* 4.2 13.7 - - + +
199B SER* 4.3 0.2 - - - -
200B LEU* 3.8 33.7 - - + -
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Residues in contact with ARG 171 (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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119B ALA 3.8 2.7 - - - -
120B PRO 3.9 9.9 - - - +
121B ARG* 3.3 22.6 + - - +
123B VAL 3.0 20.4 - - - +
124B GLU* 3.1 32.4 + - - +
125B ARG* 5.1 2.9 - - + +
169B PHE* 3.7 8.4 - - + -
170B ALA* 1.3 75.2 - - - +
172B LEU* 1.3 72.2 + - - +
173B ALA* 4.5 20.4 - - - +
192B LEU* 3.7 26.6 - - - +
196B CYS* 3.6 23.0 - - - +
200B LEU* 5.9 0.2 - - - +
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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