Contacts of the helix formed by residues 123 - 133 (chain K) in PDB entry 4PHZ
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 SER 123 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39J LEU* 4.3 8.7 - - - -
40J GLY* 4.9 1.8 - - - -
43J HIS* 2.6 32.3 + - - -
104J GLY* 3.6 18.5 + - - -
118K ILE 3.7 0.6 + - - -
119K TYR* 3.0 32.3 + - - -
122K ALA* 1.3 81.5 - - - +
124K PHE* 1.3 59.2 + - - +
125K PHE 3.6 0.7 - - - -
126K THR 3.2 1.0 + - - -
127K GLU* 2.9 34.8 + - - +
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Residues in contact with PHE 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J GLY 5.7 0.2 - - - -
107J ILE* 4.1 15.3 - - + -
108J ASN* 2.8 23.5 - - - +
111J VAL* 3.8 22.0 - - + -
112J ASN* 3.7 29.6 - - - -
39K ARG* 3.8 18.2 - - + -
119K TYR* 3.2 34.8 + + + -
120K TRP* 3.5 30.3 - + + +
123K SER* 1.3 78.9 - - - +
125K PHE* 1.3 97.3 + + - +
128K GLN* 3.1 18.6 + - - +
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Residues in contact with PHE 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K TYR* 3.6 31.6 - + - -
38K VAL* 4.4 8.3 - - + -
39K ARG* 4.7 1.1 - - + -
42K GLU* 3.4 17.9 - - - -
120K TRP* 2.9 51.9 + + + +
121K GLY 4.4 0.2 - - - -
124K PHE* 1.3 100.9 - + - +
126K THR* 1.3 59.6 + - - +
128K GLN* 3.4 21.5 - - - +
129K ASP* 3.8 9.5 + - - +
145K SER* 4.2 2.6 + - - +
148K ILE* 3.5 25.4 - - + -
149K GLU* 3.3 25.9 - - + +
153K SER* 3.8 26.7 - - - +
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Residues in contact with THR 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J HIS* 5.9 0.4 - - - +
44J VAL* 4.1 12.6 - - + -
47J MET* 3.3 35.6 - - + +
48J LEU* 6.0 2.0 - - + -
121K GLY 2.8 19.9 + - - -
122K ALA 3.4 22.2 - - - +
123K SER 3.2 0.8 + - - +
124K PHE 3.1 0.8 - - - -
125K PHE* 1.3 76.9 - - - +
127K GLU* 1.3 65.1 + - - +
128K GLN 3.1 2.0 + - - -
129K ASP* 3.5 10.9 + - - +
130K GLY 3.9 0.2 + - - -
149K GLU* 3.2 22.3 + - - +
154K TYR* 2.9 17.9 + - - +
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Residues in contact with GLU 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J HIS* 3.1 41.2 + - + +
47J MET* 3.9 13.8 - - + +
55J PHE* 3.6 21.3 - - + -
105J GLU* 3.4 3.3 - - - +
108J ASN* 3.0 35.2 + - - +
109J ARG* 2.9 41.1 + - - -
113J PHE* 3.3 21.7 - - - -
123K SER 2.9 8.7 + - - +
126K THR* 1.3 76.0 - - - +
128K GLN* 1.3 64.2 + - - +
129K ASP 3.3 0.2 - - - -
130K GLY* 3.2 10.0 + - - -
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Residues in contact with GLN 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J ASN* 3.6 8.3 - - - +
112J ASN* 3.0 34.7 + - + +
116J TRP* 3.7 24.0 - - + -
39K ARG* 3.7 5.9 - - - +
42K GLU* 2.6 39.5 + - - +
124K PHE* 3.1 22.6 + - - +
125K PHE* 3.4 18.8 - - - -
127K GLU* 1.3 78.1 - - - +
129K ASP* 1.3 58.1 + - - +
131K THR* 2.9 33.8 + - - +
132K TRP* 3.3 2.8 + - - +
145K SER* 3.5 14.7 + - - +
148K ILE* 5.2 0.7 - - - +
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Residues in contact with ASP 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J MET* 5.8 0.9 - - + -
125K PHE 3.8 1.6 + - - +
126K THR 3.5 10.4 + - - +
128K GLN* 1.3 79.3 - - - +
130K GLY* 1.3 60.3 + - - +
132K TRP* 3.9 4.5 - - - +
133K HIS* 2.8 40.9 + - - -
143K THR* 4.3 1.4 + - - -
145K SER* 3.1 26.8 + - - +
146K HIS* 3.0 17.7 + - - -
149K GLU* 3.4 26.2 - - - +
150K PHE* 4.9 0.2 - - - -
301K CU 1.7 33.9 - - - -
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Residues in contact with GLY 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J MET* 4.8 6.6 - - - +
55J PHE* 4.0 22.7 - - - -
56J TRP* 4.9 1.2 - - - -
113J PHE* 4.1 6.6 - - - -
126K THR 3.9 2.0 + - - -
127K GLU 3.2 11.9 + - - -
128K GLN 3.0 1.8 + - - -
129K ASP* 1.3 79.6 - - - +
131K THR* 1.3 58.5 + - - +
133K HIS* 3.7 17.6 + - - +
134K MET* 3.8 14.9 - - - +
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Residues in contact with THR 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J ASN* 4.0 19.5 - - + +
113J PHE* 3.4 40.5 - - + -
116J TRP* 4.3 6.3 - - + -
117J THR* 2.6 33.5 + - + +
119J PHE* 3.4 7.8 - - - -
128K GLN 2.9 21.9 + - - +
130K GLY* 1.3 74.3 - - - +
132K TRP* 1.3 64.8 + - - +
133K HIS 3.2 1.6 - - - -
134K MET* 3.2 17.0 + - - +
135K THR* 3.3 13.8 + - - -
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Residues in contact with TRP 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J TRP* 3.4 46.0 - + + -
117J THR* 4.2 3.1 - - + -
46K GLY* 3.7 25.4 - - - -
47K TRP* 4.5 11.9 - + - -
50K GLY 3.1 23.8 + - - -
51K LEU* 3.9 18.6 - - + -
128K GLN 3.3 2.7 + - - +
129K ASP* 3.5 8.3 + - - +
131K THR* 1.3 82.0 - - - +
133K HIS* 1.3 62.6 + + - +
134K MET 3.1 0.2 - - - -
135K THR* 3.2 29.2 + - + -
136K VAL* 3.3 36.2 + - + +
143K THR* 3.8 20.1 - - + -
144K PRO* 3.6 24.2 - - + +
145K SER* 4.1 16.8 - - - -
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Residues in contact with HIS 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196J THR* 2.9 14.6 + - - -
197J SER* 3.1 11.8 + - - +
129K ASP* 2.8 36.6 + - - +
130K GLY* 3.7 11.2 - - - +
131K THR 3.2 0.6 - - - -
132K TRP* 1.3 78.3 - + - +
134K MET* 1.3 68.2 + - + +
135K THR 3.2 0.9 - - - -
136K VAL* 3.0 12.5 - - - +
138K ARG* 3.4 39.8 - - - +
143K THR* 5.9 0.9 - - + -
146K HIS* 3.8 5.8 - + - -
301K CU 2.3 28.6 - - - -
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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