Contacts of the strand formed by residues 150 - 158 (chain A) in PDB entry 4R7X
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 VAL 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.3 18.9 - - + +
140A ALA 3.6 1.4 - - - +
141A GLU* 3.6 0.3 - - - -
142A LEU* 2.9 44.4 + - + +
144A ARG* 4.1 19.7 - - - +
148A LEU 3.6 11.0 - - - +
149A PRO* 1.3 77.4 - - - +
151A LYS* 1.3 70.1 + - - +
77B GLU* 4.8 13.5 - - + +
78B GLU 3.4 7.6 - - - +
79B VAL* 4.1 18.4 - - + -
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Residues in contact with LYS 151 (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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9A LEU* 4.9 0.4 - - - -
139A LYS* 3.9 23.1 - - + +
140A ALA 3.2 4.3 - - - +
141A GLU* 3.4 33.4 - - + -
143A HIS* 5.3 0.7 - - - -
149A PRO* 5.2 6.7 - - + -
150A VAL* 1.3 84.2 - - - +
152A LEU* 1.3 60.8 + - - +
153A LYS 4.2 0.2 - - - -
203A PO4 2.8 31.2 + - - +
52B ARG* 3.5 1.6 - - - +
77B GLU* 3.3 8.6 - - - +
78B GLU* 2.7 52.1 + - + +
80B GLU* 2.6 36.4 + - + +
205B PO4 3.1 21.8 + - - -
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Residues in contact with LEU 152 (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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9A LEU* 3.3 40.4 - - + +
10A THR* 4.3 1.1 - - - -
11A ILE* 3.6 36.5 - - + +
139A LYS* 3.4 3.0 - - - -
140A ALA* 2.9 36.4 + - + +
151A LYS* 1.3 74.9 - - - +
153A LYS* 1.3 65.3 + - - +
154A LYS* 4.4 5.4 - - + +
59B TRP* 4.0 26.0 - - + -
75B TYR* 4.7 8.5 - - + -
76B THR 3.3 19.3 - - - +
77B GLU* 4.2 10.1 - - + +
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Residues in contact with LYS 153 (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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137A TRP* 3.4 58.1 - - + -
138A VAL 3.6 2.7 - - - -
139A LYS* 3.8 18.4 - - + -
151A LYS 4.2 0.2 - - - -
152A LEU* 1.3 73.4 - - - +
154A LYS* 1.3 60.6 + - - +
155A GLU* 4.2 0.4 + - + -
201A PO4 2.7 33.5 + - - +
56B LYS* 4.4 8.7 - - - +
74B ASN 4.0 0.5 - - - +
75B TYR* 3.5 5.7 - - - +
76B THR* 2.6 68.5 + - + +
78B GLU* 4.0 13.9 + - - +
202B PO4 5.9 0.4 + - - -
203B PO4 4.7 3.6 + - - +
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Residues in contact with LYS 154 (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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11A ILE* 2.7 45.2 + - + +
12A SER* 4.3 4.9 - - - +
13A PHE* 3.5 34.4 - - + +
22A PRO* 5.4 1.7 - - - +
137A TRP* 3.3 2.8 - - - -
138A VAL* 2.9 35.9 + - - +
152A LEU* 3.9 2.4 + - + -
153A LYS* 1.3 74.3 - - - +
155A GLU* 1.3 58.6 + - - +
156A PHE 3.9 0.2 + - - -
73B GLN* 3.4 28.3 - - - +
74B ASN 3.9 2.2 - - - -
75B TYR* 3.4 41.8 + - + -
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Residues in contact with GLU 155 (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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13A PHE* 4.0 4.2 - - - -
22A PRO* 4.9 0.2 - - - +
126A SER* 5.6 5.0 + - - -
128A GLU* 4.1 12.6 - - - +
134A VAL 5.3 0.9 - - - +
135A ARG* 4.1 28.5 - - + +
136A TYR 3.2 15.9 - - - +
137A TRP* 3.9 6.3 - - + -
153A LYS* 4.2 0.6 + - + -
154A LYS* 1.3 73.6 - - - +
156A PHE* 1.3 70.9 + - - +
157A THR* 5.3 3.4 + - - +
73B GLN* 2.5 31.1 + - - +
74B ASN* 3.3 47.4 + - + +
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Residues in contact with PHE 156 (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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13A PHE* 4.0 16.4 - + + -
22A PRO* 3.7 17.9 - - + +
24A TYR* 3.7 21.8 - + + -
30A VAL* 4.3 12.8 - - + -
51A ALA* 5.3 0.2 - - + -
52A ARG 5.1 0.9 - - - -
82A PHE* 5.1 4.3 - + - -
116A PHE* 4.5 13.7 - + - -
118A LEU* 4.6 8.5 - - + -
126A SER* 4.2 1.4 + - - -
136A TYR* 3.1 42.1 + + + +
137A TRP* 3.6 23.6 - - - -
138A VAL* 3.5 33.0 - - + -
155A GLU* 1.3 80.8 - - - +
157A THR* 1.3 61.7 + - - +
158A VAL* 3.5 26.4 + - + -
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Residues in contact with THR 157 (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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21A VAL* 5.8 2.0 - - - +
22A PRO 2.9 14.7 + - - +
23A VAL* 3.3 21.6 - - + +
24A TYR* 2.8 27.1 + - - -
125A THR* 6.3 0.4 - - + -
126A SER* 3.7 20.3 + - - +
155A GLU* 5.3 4.6 + - - +
156A PHE* 1.3 73.5 - - - +
158A VAL* 1.3 72.1 + - - +
159A PHE* 4.2 4.0 - - + -
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Residues in contact with VAL 158 (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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24A TYR* 3.3 10.1 - - + +
25A SER* 4.7 5.4 - - - -
118A LEU* 4.0 16.4 - - + -
123A LEU* 4.3 12.8 - - + -
124A ALA 3.9 14.4 - - - +
125A THR* 3.4 2.9 - - - +
126A SER* 2.9 34.7 + - - -
136A TYR* 3.6 33.9 - - + +
156A PHE* 3.5 30.7 + - + -
157A THR* 1.3 74.3 - - - +
159A PHE* 1.3 67.1 + - - +
160A GLU* 4.8 3.1 - - - +
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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