Contacts of the strand formed by residues 163 - 171 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A HIS* 4.2 17.0 - - + -
60A ARG* 4.1 35.0 - - + +
63A VAL* 4.1 18.6 - - + -
111A ALA 4.8 1.6 - - - +
113A ILE* 3.7 25.1 - - + -
159A GLU* 3.1 3.3 - - - -
160A PHE 2.9 35.5 + - - +
162A GLY* 1.3 83.4 - - - +
164A GLU* 1.3 76.7 + - - +
165A ILE* 3.2 20.2 + - + +
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLY 4.9 7.1 - - - +
111A ALA 5.0 1.4 + - - -
112A ASP* 3.3 32.0 - - + +
113A ILE 2.8 25.3 + - - -
146A ARG* 5.9 4.9 + - - +
158A PHE 3.6 6.1 - - - +
159A GLU* 4.3 19.3 - - + +
162A GLY 3.8 4.1 + - - +
163A ILE* 1.3 73.9 - - - +
165A ILE* 1.3 61.8 + - - +
166A ASP* 5.3 3.3 - - - +
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 4.1 24.7 - - + -
64A LEU* 5.0 9.2 - - + -
67A LEU* 3.9 26.9 - - + -
113A ILE* 3.5 13.9 - - + +
115A ALA* 4.6 6.1 - - + -
156A ILE 3.9 0.5 - - - +
157A LYS* 3.4 2.4 - - - +
158A PHE* 2.7 62.2 + - + +
160A PHE* 4.1 11.4 - - + -
163A ILE* 3.6 17.0 - - + +
164A GLU* 1.3 80.6 - - - +
166A ASP* 1.3 72.1 + - - +
167A LEU* 3.8 9.6 - - + +
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Residues in contact with ASP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 5.2 1.6 - - - -
112A ASP* 4.8 13.8 - - - +
113A ILE 3.0 9.6 + - - +
114A ASP* 3.6 23.3 - - - +
115A ALA 3.0 24.2 + - - +
146A ARG* 5.6 0.3 + - - -
155A VAL* 3.8 10.3 - - + +
156A ILE 3.8 3.4 - - - -
157A LYS* 2.6 43.0 + - - +
164A GLU* 5.0 3.8 - - - +
165A ILE* 1.3 80.1 + - - +
167A LEU* 1.3 60.5 + - - +
168A VAL* 3.8 2.4 + - - +
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 4.3 14.4 - - + -
71A VAL* 5.0 0.9 - - + -
96A ILE* 4.4 8.1 - - + -
115A ALA* 3.5 26.0 - - + +
116A LEU 4.0 1.1 - - - +
117A CYS* 3.8 21.5 - - + +
128A PHE* 3.7 21.5 - - + -
132A PHE* 3.7 34.1 - - + -
136A LEU* 5.0 0.7 - - + -
155A VAL* 3.4 2.7 - - - +
156A ILE* 2.8 46.9 + - + +
158A PHE* 4.0 17.3 - - + -
165A ILE* 3.8 5.1 - - + -
166A ASP* 1.3 71.6 - - - +
168A VAL* 1.3 67.7 + - - +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 4.6 13.9 - - + -
115A ALA 2.8 13.6 + - - +
116A LEU* 3.3 23.7 - - + -
117A CYS* 2.6 34.7 + - - +
128A PHE* 4.6 1.1 - - - -
153A VAL* 3.8 23.8 - - + -
154A PRO 3.0 26.7 - - - +
155A VAL* 4.2 9.6 - - + -
166A ASP 4.7 2.5 - - - +
167A LEU* 1.3 74.5 - - - +
169A PHE* 1.3 56.4 + - - +
199A SER* 3.8 16.2 - - - +
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A TRP* 3.6 20.9 - + - -
116A LEU* 4.3 0.7 - - - -
117A CYS* 3.6 18.8 - - - -
119A ALA* 3.5 30.7 - - + -
123A VAL* 3.9 15.5 - - + -
124A GLU 4.4 0.2 - - - -
125A ARG* 3.3 43.2 + - + +
128A PHE* 3.5 48.7 - + + -
129A PHE* 5.3 0.7 - + + -
154A PRO 4.2 4.6 + - - +
168A VAL* 1.3 79.8 - - - +
170A ALA* 1.3 84.8 + - - +
171A ARG* 3.8 12.1 - - + -
199A SER* 2.9 23.9 + - - -
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.0 10.5 - - + +
117A CYS 2.9 9.3 + - - +
118A VAL* 3.7 5.1 - - + +
119A ALA 3.2 24.3 + - - -
169A PHE* 1.3 85.8 - - - +
171A ARG* 1.3 60.8 + - - +
172A LEU* 4.1 2.4 + - + -
196A CYS* 4.2 13.0 - - + +
199A SER* 4.2 1.6 - - - -
200A LEU* 3.7 34.5 - - + -
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ALA 4.1 4.3 - - - -
120A PRO 4.5 2.5 - - - +
121A ARG* 3.4 26.1 + - - +
122A HIS 5.2 0.6 - - - -
123A VAL 3.3 25.8 + - - +
124A GLU* 2.7 41.4 + - - +
125A ARG* 4.7 5.6 - - + +
169A PHE* 3.8 10.2 - - + -
170A ALA* 1.3 72.3 - - - +
172A LEU* 1.3 73.2 + - - +
173A ALA* 4.3 4.1 + - - +
192A LEU* 4.4 9.4 - - - +
196A CYS* 3.5 32.0 - - - +
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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