Contacts of the strand formed by residues 144 - 156 (chain E) 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 GLY 144 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139E ASN* 3.3 6.7 - - - -
140E VAL* 2.8 39.6 + - - +
141E GLU 4.7 0.6 + - - -
143E GLY* 1.3 74.8 - - - +
145E PRO* 1.4 73.8 - - - +
146E ILE* 3.6 1.9 + - - +
201F TYR* 5.1 2.2 - - - -
210J LEU* 4.1 5.5 - - - +
211J ARG* 4.0 16.2 - - - +
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Residues in contact with PRO 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E GLN* 3.4 20.9 + - - +
137E GLN* 4.5 4.9 - - - +
138E ILE 3.9 0.2 - - - +
139E ASN* 3.2 21.5 - - - +
144E GLY* 1.4 84.3 - - - +
146E ILE* 1.3 63.7 + - - +
147E ILE* 4.1 10.5 - - + -
196F THR 5.7 0.7 - - - +
137G ILE* 3.5 34.1 - - + -
210J LEU* 3.9 21.0 - - - +
211J ARG* 4.5 13.0 - - + +
213J PHE* 5.5 1.6 - - + -
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Residues in contact with ILE 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E GLN* 4.9 1.1 - - - -
39E ARG* 5.4 7.4 - - + +
42E THR* 3.9 27.4 - - + +
43E LEU* 3.9 37.9 - - + +
45E TRP* 3.6 12.6 - - - +
73E TRP* 4.4 4.0 - - + -
137E GLN* 3.6 2.9 - - - +
138E ILE 2.7 38.3 + - - +
140E VAL* 3.8 28.7 - - + -
144E GLY 4.2 1.1 - - - +
145E PRO* 1.3 76.6 - - - +
147E ILE* 1.3 65.7 + - - +
210J LEU* 3.7 24.9 - - + -
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Residues in contact with ILE 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E HIS 5.1 2.7 - - - +
30E GLY 5.5 1.1 - - - +
31E GLU* 3.5 36.4 - - + +
34E GLN* 3.5 21.4 + - - +
45E TRP* 3.6 9.3 + - - -
88E GLY* 6.0 0.4 - - - -
135E HIS* 3.4 37.5 - - + +
136E ALA 4.0 1.6 - - - +
137E GLN* 3.8 29.2 - - + +
145E PRO* 4.1 14.4 - - + -
146E ILE* 1.3 75.8 - - - +
148E GLY* 1.3 61.9 + - - +
322E ALA 4.3 8.3 - - - +
137G ILE* 4.1 19.3 - - + -
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Residues in contact with GLY 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E GLU* 5.2 1.6 - - - -
45E TRP* 3.3 21.9 - - - -
135E HIS* 2.9 23.7 + - - -
136E ALA 2.5 21.7 + - - -
147E ILE* 1.3 76.7 - - - +
149E PRO* 1.3 74.0 - - - +
322E ALA 5.2 2.5 - - - -
341E TYR* 4.3 1.2 + - - -
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Residues in contact with PRO 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E TRP* 3.7 24.2 - - + +
48E VAL* 3.7 22.6 - - + +
50E TRP* 3.5 24.4 - - + -
135E HIS* 3.4 0.2 - - - -
136E ALA* 3.2 24.4 + - + +
148E GLY* 1.3 83.6 - - - +
150E GLY* 1.3 59.2 + - - +
323E GLY* 3.9 19.5 - - - -
338E PHE* 4.0 13.7 - - + -
341E TYR* 3.9 0.9 - - - +
342E LEU* 3.6 20.9 - - + -
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Residues in contact with GLY 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E TRP* 3.6 2.2 - - - -
133E HIS* 3.2 16.2 + - - -
134E VAL 3.2 12.1 - - - -
135E HIS* 3.4 21.0 + - - -
149E PRO* 1.3 75.4 - - - +
151E GLN* 1.3 60.5 + - - -
339E PRO* 3.4 10.2 - - - +
341E TYR* 3.0 22.4 + - - -
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Residues in contact with GLN 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E TRP* 3.3 42.9 - - + +
53E THR* 4.4 14.8 - - + +
133E HIS* 3.4 6.9 + - - -
134E VAL 2.9 24.5 + - - +
150E GLY* 1.3 72.7 - - - +
152E TRP* 1.3 105.6 + - - +
153E ILE* 3.5 10.1 - - + +
337E ASP* 5.3 5.1 + - - -
338E PHE 4.7 1.2 - - - -
339E PRO* 3.4 35.0 - - - +
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Residues in contact with TRP 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E HIS* 4.0 17.9 - + - -
53E THR* 3.9 10.8 - - - +
131E ARG* 3.3 81.0 - - + +
132E TRP* 3.3 17.7 - - - -
133E HIS* 3.3 39.6 + + + -
151E GLN* 1.3 95.7 + - - +
153E ILE* 1.3 67.0 + - - +
154E GLU 4.2 0.9 - - - +
341E TYR* 6.0 2.0 - + - -
48G ARG* 5.6 1.8 - - - -
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Residues in contact with ILE 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E TRP* 3.8 25.1 - - + -
52E LYS 3.6 20.2 - - - +
53E THR* 3.6 12.8 - - - -
54E THR 4.7 0.2 - - - +
55E VAL* 4.3 16.4 - - + -
61E MET* 4.2 17.5 - - - -
94E LEU* 4.5 6.7 - - + -
130E GLY 3.7 1.2 - - - +
131E ARG* 4.7 0.9 - - - -
132E TRP* 2.8 35.0 + - - +
134E VAL* 3.8 22.4 - - + -
151E GLN* 3.5 14.4 - - + +
152E TRP* 1.3 85.9 - - - +
154E GLU* 1.3 73.0 + - - +
155E ILE* 3.8 4.5 + - + +
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Residues in contact with GLU 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E THR 3.1 14.0 + - - +
54E THR* 3.4 13.4 + - + +
55E VAL* 2.9 26.6 + - - +
130E GLY 3.4 9.9 - - - +
131E ARG* 4.4 26.2 + - + +
152E TRP* 4.2 0.6 - - - +
153E ILE* 1.3 72.8 - - - +
155E ILE* 1.3 66.1 + - - +
156E LYS* 3.3 32.7 + - - +
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Residues in contact with ILE 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E VAL* 3.2 19.1 - - + +
57E VAL* 4.0 27.4 - - + +
93E VAL 3.5 21.8 - - - +
94E LEU* 3.8 22.0 - - + -
126E GLY* 4.2 11.0 - - - -
127E ARG 4.3 0.7 - - - +
128E ARG 3.6 16.6 - - - +
129E ALA* 3.4 4.7 - - - +
130E GLY* 2.8 27.2 + - - +
132E TRP* 3.3 26.2 - - + -
153E ILE* 4.1 6.3 - - + +
154E GLU* 1.3 81.7 - - - +
156E LYS* 1.3 68.4 + - - +
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Residues in contact with LYS 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E THR* 4.4 18.8 - - + -
55E VAL 2.8 10.3 + - - +
56E ASN* 3.2 22.2 - - - +
57E VAL* 2.7 34.6 + - - +
129E ALA* 4.7 1.1 - - - -
154E GLU* 3.3 39.4 + - - +
155E ILE* 1.3 78.2 + - - +
157E GLY* 1.3 57.6 + - - +
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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