Contacts of the strand formed by residues 123 - 133 (chain A) in PDB entry 4TZM
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 GLU 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ARG* 2.9 46.5 + - - +
59A ILE* 5.2 1.0 - - - +
110A LEU 3.9 0.9 - - - +
111A VAL* 3.8 0.2 - - - -
112A VAL* 2.8 47.9 + - + +
121A ALA 3.5 1.0 - - - -
122A ILE* 1.3 87.7 - - + +
124A VAL* 1.3 68.0 + - - +
125A PHE* 3.6 26.6 - - + -
186A LEU* 3.9 2.2 - - - +
189A LEU* 3.7 16.6 - - + +
227A ILE* 5.1 0.4 - - - -
247A TRP 3.4 13.5 - - - +
248A SER* 2.7 22.7 + - - +
250A SER* 3.8 1.7 + - - +
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Residues in contact with VAL 124 (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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109A SER* 4.1 11.2 - - - -
110A LEU 3.4 3.8 - - - +
111A VAL* 4.3 7.9 - - + -
121A ALA* 3.6 21.1 - - + -
123A GLU* 1.3 80.3 - - - +
125A PHE* 1.3 75.8 + - - +
126A SER 4.1 1.1 - - - +
221A TYR* 3.8 42.8 - - + +
223A LEU* 4.1 8.1 - - + -
227A ILE* 6.3 0.2 - - + -
245A GLN 3.7 0.3 - - - +
246A CYS* 3.2 7.3 - - - -
247A TRP* 2.8 52.3 + - + +
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Residues in contact with PHE 125 (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 PHE* 3.5 7.1 - - + -
53A VAL* 3.5 40.4 - - + -
57A ARG* 4.2 2.7 - - + -
109A SER* 3.3 1.6 - - - -
110A LEU* 2.8 48.6 + - + -
112A VAL* 6.1 1.6 - - + -
123A GLU* 3.6 27.4 - - + -
124A VAL* 1.3 75.3 - - - +
126A SER* 1.3 59.9 + - - +
178A VAL* 5.3 3.1 - - + -
181A LEU* 3.9 11.4 - - + -
182A CYS* 4.0 15.7 - - - -
186A LEU* 4.0 14.4 - - + -
232A ILE* 4.6 5.4 - - + -
244A MET* 3.9 20.6 - - + -
245A GLN 3.5 2.9 - - - -
246A CYS* 3.5 35.9 - - + -
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Residues in contact with SER 126 (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 PHE* 4.9 0.2 - - - -
107A GLU* 3.2 15.0 - - - -
108A ILE 3.8 0.2 - - - -
109A SER* 3.1 22.4 - - - -
124A VAL* 4.0 5.1 - - - -
125A PHE* 1.3 73.2 - - - +
127A MET* 1.3 59.6 + - - +
128A LYS* 4.5 4.6 - - - +
221A TYR* 3.9 6.5 - - - -
243A HIS 3.4 1.9 + - - +
244A MET* 3.2 10.5 - - - +
245A GLN* 2.9 43.3 + - - +
247A TRP* 3.4 19.8 - - - -
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Residues in contact with MET 127 (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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42A MET* 6.2 0.4 - - - +
45A ALA* 5.0 2.2 - - - -
46A ILE* 4.0 18.4 - - - -
49A VAL* 4.1 24.5 - - + -
50A PHE* 3.6 22.9 - - + -
107A GLU* 3.4 0.4 - - - -
108A ILE* 3.0 39.7 + - + +
126A SER* 1.3 73.4 - - - +
128A LYS* 1.3 62.8 + - - +
129A PHE* 3.3 35.5 - - + -
174A ILE* 6.5 0.7 - - + -
235A LEU* 5.3 7.9 - - + -
242A ALA* 4.0 17.3 - - + -
243A HIS 3.4 6.5 - - - +
244A MET* 3.6 24.0 - - + -
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Residues in contact with LYS 128 (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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106A LYS* 3.5 16.4 - - - +
107A GLU* 3.3 41.1 - - + +
126A SER* 4.5 7.6 - - - +
127A MET* 1.3 74.3 - - - +
129A PHE* 1.3 62.6 + - - +
150A ASP* 4.4 18.7 + - - +
151A PRO* 5.6 3.4 - - - +
152A HIS* 3.5 36.5 + - + +
156A LEU* 5.1 0.9 - - - +
221A TYR* 4.8 1.1 - - - -
242A ALA* 3.1 4.7 - - - -
243A HIS* 2.7 43.3 + - + +
245A GLN* 3.9 14.8 + - - +
247A TRP* 3.9 20.3 - - - -
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Residues in contact with PHE 129 (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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42A MET* 4.3 21.8 - - + -
46A ILE* 3.8 22.4 - - + -
100A THR* 4.2 15.0 - - + -
105A LEU* 3.7 43.7 - - + +
106A LYS* 2.8 31.6 + - - +
108A ILE* 4.0 5.2 - - + -
127A MET* 3.3 40.4 - - + -
128A LYS* 1.3 73.5 - - - +
130A ILE* 1.3 70.0 + - - +
131A TYR* 4.2 16.8 - + + +
152A HIS* 5.3 1.2 + - - -
153A PHE* 5.7 0.9 - - - -
240A HIS* 5.7 2.2 - + + -
241A ALA 3.2 13.2 - - - -
242A ALA* 3.9 15.9 - - + -
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Residues in contact with ILE 130 (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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128A LYS 5.4 0.2 - - - +
129A PHE* 1.3 80.8 - - - +
131A TYR* 1.3 74.3 + - - +
132A PHE* 3.9 16.4 - - + -
139A ALA* 4.0 17.7 - - + -
140A ARG 5.2 2.0 - - - +
152A HIS* 4.5 8.1 - - + +
153A PHE* 3.9 37.7 - - + +
156A LEU* 3.7 42.8 - - + -
157A ALA 3.9 9.4 - - - +
240A HIS* 3.5 6.1 - - - +
241A ALA* 2.8 36.1 + - + +
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Residues in contact with TYR 131 (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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100A THR* 3.4 39.5 - - + +
103A GLY* 3.6 26.9 - - - -
105A LEU* 2.6 43.7 + - - +
106A LYS* 5.2 0.2 - - - -
129A PHE* 4.2 15.8 - + + +
130A ILE* 1.3 79.3 - - - +
132A PHE* 1.3 62.2 + - - +
139A ALA* 3.5 4.5 - - - -
140A ARG* 2.9 58.2 + - + +
202A THR* 4.2 8.3 - - + -
204A ASP* 6.0 0.4 - - - -
239A HIS 4.1 1.3 - - - +
240A HIS* 3.4 25.1 - + - -
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Residues in contact with PHE 132 (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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130A ILE* 3.9 18.8 - - + -
131A TYR* 1.3 75.7 - - - +
133A GLU* 1.3 61.7 + - - +
136A GLY* 3.6 21.0 - - - +
137A VAL 3.4 20.9 - - - -
138A VAL 3.3 4.0 - - - +
139A ALA* 3.5 18.4 - - + -
140A ARG* 4.4 9.8 + - - -
156A LEU 3.9 10.8 - - - -
157A ALA* 3.2 27.8 - - - -
236A ARG* 3.4 35.9 - - - -
239A HIS* 3.1 33.7 + - - +
241A ALA* 3.6 25.1 - - + -
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Residues in contact with GLU 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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132A PHE* 1.3 74.8 - - - +
134A ASN* 1.3 75.7 + - + +
135A GLY 3.6 1.3 - - - -
136A GLY 3.7 2.5 - - - +
137A VAL 3.1 3.6 + - - -
138A VAL* 2.7 52.0 + - + +
139A ALA 4.2 4.5 - - - +
140A ARG* 3.3 38.3 - - + +
239A HIS* 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