Contacts of the helix formed by residues 120 - 135 (chain A) in PDB entry 2PWZ
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 PRO 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A PHE* 3.9 34.1 - - + -
94A ASN* 5.2 2.9 - - + +
119A ASN* 1.3 83.8 - - + +
121A VAL* 1.3 52.4 + - - +
122A ASN* 3.2 6.3 - - + +
123A THR* 2.9 22.1 + - - +
124A THR* 2.8 38.2 + - + +
178A SER* 5.7 8.5 - - - +
302A ASP* 6.5 0.7 - - - -
305A LEU* 6.2 0.2 - - + -
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Residues in contact with VAL 121 (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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116A ILE* 3.6 18.4 - - + +
117A ILE 3.6 7.4 - - - +
118A THR 3.4 15.7 - - - +
119A ASN* 3.2 15.3 + - - +
120A PRO* 1.3 70.7 - - - +
122A ASN* 1.3 63.1 + - - +
123A THR 3.2 0.9 + - - -
124A THR* 3.3 7.0 - - - +
125A VAL* 3.0 30.0 + - + +
145A GLY* 3.5 31.4 - - - -
146A VAL 4.2 3.8 - - - +
147A THR* 4.7 0.4 - - + -
177A HIS* 3.8 32.4 - - + +
253A TYR* 3.5 11.3 - - + -
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Residues in contact with ASN 122 (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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120A PRO* 3.2 5.4 + - + +
121A VAL* 1.3 75.7 - - - +
123A THR* 1.3 59.4 + - - +
126A ALA* 4.3 4.0 - - - +
176A GLY* 3.1 8.1 - - - -
177A HIS* 2.8 26.9 + - - +
178A SER* 3.9 10.8 + - - +
181A THR* 3.0 25.3 + - - +
253A TYR* 2.9 32.0 + - - +
299A LEU* 3.8 14.2 - - + +
302A ASP* 3.2 35.8 + - + +
303A ILE* 4.0 12.0 - - - +
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Residues in contact with THR 123 (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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91A PHE* 3.6 29.4 - - + -
120A PRO* 2.9 21.3 + - - +
122A ASN* 1.3 76.5 - - - +
124A THR* 1.3 56.6 + - - +
125A VAL 3.4 1.8 - - - -
126A ALA* 3.1 8.4 + - - +
127A ILE* 3.0 27.0 + - + +
302A ASP* 2.4 30.9 + - - +
305A LEU* 3.9 9.9 - - + +
306A GLY* 3.5 27.0 - - - +
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Residues in contact with THR 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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91A PHE* 5.4 0.2 - - + -
94A ASN 4.9 0.2 - - - +
95A ALA* 4.8 8.1 - - + +
98A VAL* 3.7 24.8 - - + +
116A ILE* 3.3 12.0 - - - +
118A THR* 2.9 28.2 + - + +
119A ASN 4.1 4.9 - - - +
120A PRO* 2.8 36.5 + - + +
121A VAL* 3.3 7.3 - - - -
123A THR* 1.3 70.3 - - + +
125A VAL* 1.3 60.4 + - - +
126A ALA 3.3 0.2 - - - -
127A ILE* 3.5 20.6 - - + +
128A ALA* 3.1 25.5 + - - +
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Residues in contact with VAL 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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116A ILE* 3.8 19.5 - - + -
121A VAL* 3.0 21.7 + - + +
124A THR* 1.3 74.2 - - - +
126A ALA* 1.3 62.5 + - - +
128A ALA* 4.1 4.9 - - - -
129A ALA* 3.0 24.3 + - - +
143A LEU* 3.4 17.3 - - + +
145A GLY* 3.4 32.1 - - - +
253A TYR* 3.5 32.3 - - + +
254A VAL* 5.5 0.2 - - - -
263A PHE* 3.6 20.4 - - + -
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Residues in contact with ALA 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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122A ASN 4.3 4.4 + - - +
123A THR 3.1 12.6 + - - +
125A VAL* 1.3 78.3 - - - +
127A ILE* 1.3 64.5 + - - +
129A ALA* 3.4 2.1 + - - +
130A GLU* 3.1 28.3 + - - +
262A ARG* 4.7 0.5 + - - -
263A PHE* 4.1 25.1 - - + -
303A ILE* 3.6 33.9 - - + +
306A GLY* 4.2 4.0 - - - -
307A GLU* 4.6 4.5 - - + -
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Residues in contact with ILE 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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95A ALA* 3.4 37.5 - - + -
98A VAL* 4.3 4.3 - - + -
99A LYS* 4.0 33.9 - - + +
123A THR* 3.0 25.5 + - + +
124A THR* 3.5 21.5 - - + +
125A VAL 3.3 0.2 - - - -
126A ALA* 1.3 74.2 - - - +
128A ALA* 1.3 53.0 + - - +
130A GLU* 3.0 5.5 + - - +
131A VAL* 2.8 34.4 + - + +
306A GLY* 3.5 19.5 - - - +
309A PHE* 4.1 9.9 - - + -
310A VAL* 3.8 17.9 - - + -
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Residues in contact with ALA 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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98A VAL* 4.5 0.4 - - + -
102A VAL* 3.6 34.4 - - + +
116A ILE* 4.0 7.4 - - + -
124A THR 3.1 13.6 + - - +
125A VAL 3.6 6.3 - - - +
126A ALA 3.3 0.2 - - - -
127A ILE* 1.3 81.3 - - - +
129A ALA* 1.3 56.6 + - - +
131A VAL* 3.4 1.6 + - - -
132A LEU* 3.0 36.0 + - - +
143A LEU* 3.8 22.0 - - + -
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Residues in contact with ALA 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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125A VAL 3.0 17.8 + - - +
126A ALA 3.7 4.0 - - - +
127A ILE 3.3 0.2 - - - -
128A ALA* 1.3 75.5 - - - +
130A GLU* 1.3 56.3 + - - +
132A LEU* 3.2 2.3 + - - +
133A LYS* 2.8 49.9 + - - +
138A TYR* 3.8 14.3 - - + -
143A LEU* 3.7 13.4 - - + +
262A ARG* 4.6 1.8 - - - +
263A PHE* 3.6 24.5 - - + -
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Residues in contact with GLU 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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126A ALA 3.1 15.2 + - - +
127A ILE 3.0 8.4 + - - +
129A ALA* 1.3 72.6 - - - +
131A VAL* 1.3 65.1 - - - +
133A LYS* 3.1 24.6 + - - +
134A LYS* 3.1 29.3 + - - +
262A ARG* 2.9 25.1 + - - -
307A GLU* 3.8 29.6 - - + +
310A VAL* 3.7 21.5 - - + -
311A ASN* 3.3 20.3 + - - +
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Residues in contact with VAL 131 (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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99A LYS* 3.9 37.5 - - + +
102A VAL* 3.6 11.2 - - + +
103A GLN* 3.5 45.0 - - + +
106A ALA* 5.1 1.3 - - + -
127A ILE 2.8 16.5 + - - +
128A ALA 3.6 7.4 - - - +
130A GLU* 1.3 78.2 - - - +
132A LEU* 1.3 62.2 + - - +
134A LYS* 3.4 7.6 + - - +
135A ALA* 3.2 19.8 + - - +
310A VAL* 4.2 12.1 - - + -
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Residues in contact with LEU 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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102A VAL* 3.8 13.9 - - + -
105A VAL* 4.8 0.9 - - + -
106A ALA* 3.9 27.8 - - + +
110A PRO 5.2 4.0 - - - +
114A ILE* 3.8 32.5 - - + -
128A ALA 3.0 29.4 + - - +
129A ALA 3.2 2.9 + - - +
131A VAL* 1.3 73.7 - - - +
133A LYS* 1.3 59.2 + - - +
135A ALA* 3.4 2.8 + - - -
136A GLY 3.1 6.2 + - - -
137A VAL* 2.9 44.0 + - + +
138A TYR* 3.8 29.8 - - + +
139A ASP 5.7 0.7 - - - +
143A LEU* 4.4 13.9 - - + -
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Residues in contact with LYS 133 (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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129A ALA* 2.8 45.0 + - - +
130A GLU* 3.1 32.3 + - - +
132A LEU* 1.3 73.6 - - - +
134A LYS* 1.3 61.7 + - - +
136A GLY* 2.9 20.5 + - - -
138A TYR* 3.7 33.3 - - + +
262A ARG* 4.0 13.3 - - - +
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Residues in contact with LYS 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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103A GLN* 6.1 0.2 - - - +
130A GLU* 3.1 16.6 + - - +
131A VAL* 3.5 7.4 - - - +
133A LYS* 1.3 77.8 - - + +
135A ALA* 1.3 58.6 + - - +
136A GLY 3.5 0.5 + - - -
310A VAL* 3.6 22.9 - - + -
311A ASN* 2.9 36.1 - - - +
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Residues in contact with ALA 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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103A GLN* 4.5 11.9 + - - +
106A ALA* 3.7 30.5 - - + +
131A VAL 3.2 10.7 + - - +
132A LEU 3.7 8.5 - - - +
133A LYS 3.1 0.8 - - - -
134A LYS* 1.3 75.4 - - - +
136A GLY* 1.3 60.3 + - - +
137A VAL* 3.5 11.2 + - + +
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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