Contacts of the strand formed by residues 132 - 143 (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 GLY 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A LYS 3.3 6.7 - - - -
57A VAL* 4.4 4.5 - - - -
127A PHE* 5.3 2.0 - - - -
129A GLY* 2.7 36.0 + - - +
130A ARG 4.0 1.2 - - - +
131A HIS* 1.3 81.7 - - - +
133A SER* 1.3 58.8 + - - -
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Residues in contact with SER 133 (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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54A HIS 3.9 0.3 - - - +
55A ALA* 3.2 4.3 - - - +
56A LYS* 2.7 47.4 + - - +
127A PHE* 3.3 20.6 - - - -
128A GLU* 3.7 17.7 - - - -
132A GLY* 1.3 76.8 - - - -
134A VAL* 1.3 63.4 + - - +
135A ARG* 3.5 27.6 + - - -
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Residues in contact with VAL 134 (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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54A HIS 3.3 13.0 - - - +
55A ALA* 4.0 17.5 - - + -
81A TYR* 4.7 3.1 - - + +
124A ALA* 4.0 19.5 - - + -
125A THR 3.5 24.7 - - - +
126A SER* 3.5 7.4 - - - -
127A PHE* 3.0 32.1 + - + +
128A GLU* 5.0 0.3 - - - +
133A SER* 1.3 77.2 - - - +
135A ARG* 1.3 66.4 + - - +
136A TYR* 3.9 22.9 - - + -
155A GLU* 5.3 0.5 - - - +
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Residues in contact with ARG 135 (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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52A ARG 4.0 0.3 - - - +
53A GLY* 3.2 2.1 - - - -
54A HIS* 3.0 38.6 + - + +
56A LYS* 4.3 5.1 - - + +
58A ARG* 3.1 31.1 - - - +
126A SER* 4.9 0.9 - - - -
128A GLU* 3.0 38.0 + - - +
133A SER* 3.5 21.1 + - - +
134A VAL* 1.3 80.1 - - - +
136A TYR* 1.3 64.7 + - - +
137A TRP* 4.6 7.4 - - + -
155A GLU* 4.1 23.8 - - - +
201A PO4 3.1 40.0 + - - +
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Residues in contact with TYR 136 (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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52A ARG 3.3 5.4 - - - -
53A GLY* 3.5 27.1 - - - -
81A TYR* 4.1 5.8 - - + +
82A PHE* 4.3 20.4 - + + -
118A LEU* 5.6 2.5 - - + -
123A LEU* 3.3 21.8 - - + +
124A ALA* 2.8 35.7 + - - +
126A SER* 3.6 17.4 + - - -
134A VAL* 3.9 15.9 - - + -
135A ARG* 1.3 78.8 - - - +
137A TRP* 1.3 65.0 + - - +
155A GLU* 3.2 9.2 + - - +
156A PHE* 3.1 54.7 + + + +
158A VAL* 3.6 27.4 - - + -
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Residues in contact with TRP 137 (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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50A HIS* 3.4 22.0 - - - -
51A ALA* 3.4 2.3 - - - -
52A ARG* 2.9 70.4 + - + -
54A HIS* 3.5 19.7 + + - -
135A ARG* 4.6 7.2 - - + -
136A TYR* 1.3 81.8 - - - +
138A VAL* 1.3 59.2 + - - +
139A LYS* 3.6 22.4 - - + -
153A LYS* 3.4 28.3 - - + -
154A LYS 3.3 15.9 - - - +
155A GLU* 3.9 5.4 - - + -
156A PHE* 3.6 10.9 - - - -
201A PO4 3.4 26.4 + - - -
203A PO4 4.1 17.7 - - - -
203B PO4 4.1 18.2 - - - -
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Residues in contact with VAL 138 (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* 3.6 16.6 - - + +
13A PHE* 3.8 26.7 - - + -
49A ILE* 4.6 15.3 - - + -
50A HIS 3.7 6.1 - - - +
51A ALA* 4.4 1.1 - - + +
114A PHE* 4.3 21.3 - - + -
116A PHE* 3.9 24.7 - - + -
137A TRP* 1.3 75.6 - - - +
139A LYS* 1.3 67.3 + - - +
154A LYS 2.9 29.4 + - - +
156A PHE* 3.5 22.4 - - + -
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Residues in contact with LYS 139 (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* 4.5 0.9 - - - -
48A LYS 3.8 0.5 - - - +
49A ILE* 3.2 7.6 - - - +
50A HIS* 2.8 48.9 + - + +
137A TRP* 3.6 20.2 - - + -
138A VAL* 1.3 75.0 - - - +
140A ALA* 1.3 62.8 + - - +
141A GLU* 4.2 6.9 - - - +
151A LYS* 3.9 16.4 - - + +
152A LEU 3.4 6.1 - - - +
153A LYS* 3.8 20.8 - - + +
203A PO4 2.9 29.7 + - - +
52B ARG* 4.0 0.6 - - - +
78B GLU* 3.0 39.9 + - - -
203B PO4 3.2 24.5 + - - -
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Residues in contact with ALA 140 (chain A).
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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9A LEU* 4.3 9.0 - - + +
11A ILE* 3.7 21.7 - - + +
34A VAL* 4.0 30.5 - - + -
47A LEU* 5.0 3.4 - - + -
48A LYS 3.6 5.6 - - - +
49A ILE* 4.7 2.0 - - + +
139A LYS* 1.3 71.2 - - - +
141A GLU* 1.3 60.7 + - - +
142A LEU 4.1 0.4 + - - -
150A VAL 3.6 1.7 - - - +
151A LYS* 3.2 5.1 - - - -
152A LEU* 2.9 38.2 + - + +
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Residues in contact with GLU 141 (chain A).
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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46A SER 3.8 0.7 - - - +
47A LEU* 3.4 9.1 - - - +
48A LYS* 2.8 54.5 + - + +
49A ILE 5.5 0.2 - - - -
50A HIS* 3.7 18.3 - - + +
139A LYS* 4.2 10.5 - - + +
140A ALA* 1.3 77.1 - - - +
142A LEU* 1.3 60.1 + - - +
143A HIS* 4.0 13.7 + - + +
149A PRO* 6.4 0.4 - - + -
150A VAL 3.6 4.0 - - - -
151A LYS* 3.4 33.8 + - + +
203A PO4 2.9 28.2 + - - -
205B PO4 3.5 16.1 + - - -
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Residues in contact with LEU 142 (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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6A VAL* 3.9 29.6 - - + -
9A LEU* 4.6 15.3 - - + -
36A LEU* 4.3 21.1 - - + -
42A ILE* 5.1 0.9 - - + -
44A VAL* 3.7 35.4 - - + -
46A SER 3.9 2.5 - - - +
47A LEU* 4.2 15.5 - - + -
89A ILE* 6.4 0.2 - - + -
140A ALA 4.1 0.4 + - - -
141A GLU* 1.3 71.9 - - - +
143A HIS* 1.3 65.2 + - - +
144A ARG* 4.0 22.2 + - + +
148A LEU 4.7 1.2 - - - +
149A PRO* 3.6 6.1 - - - +
150A VAL* 2.9 42.2 + - + +
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Residues in contact with HIS 143 (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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44A VAL* 3.6 2.4 - - - +
45A LYS* 2.7 36.8 + - + -
46A SER* 2.9 39.0 + - - +
48A LYS* 4.6 14.4 + - + +
141A GLU* 4.1 23.1 + - + +
142A LEU* 1.3 75.5 - - - +
144A ARG* 1.3 60.5 + - - +
149A PRO* 4.0 18.7 - - + +
151A LYS* 5.6 0.7 - - - -
204A PO4 3.1 38.7 + - - +
205B PO4 3.6 35.5 + - - -
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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