Contacts of the helix formed by residues 128 - 142 (chain A) in PDB entry 3PMM
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 TYR 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ASP* 4.1 10.9 + - - +
94A PHE* 4.6 13.3 - + + +
95A ALA* 6.0 0.7 - - - -
98A PHE* 4.4 17.5 - + - -
116A LEU* 3.7 35.6 - - + +
119A ARG* 4.1 13.1 - - + +
120A PHE* 3.8 28.7 - - + -
123A THR* 4.1 4.9 - - - -
125A ARG* 2.9 64.2 + - + +
127A ALA* 1.3 84.1 - - + +
129A LEU* 1.3 65.1 + - - +
130A PRO 3.5 0.2 - - - -
131A TRP* 3.2 12.5 + - - +
132A LEU* 3.2 21.9 + - + +
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Residues in contact with LEU 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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120A PHE* 4.0 21.3 - - + -
125A ARG 4.0 0.4 + - - -
126A MSE 3.1 9.3 + - - +
128A TYR* 1.3 79.8 - - - +
130A PRO* 1.4 70.4 - - + +
132A LEU* 3.1 8.1 + - + +
133A GLU* 2.9 53.0 + - + +
183A LEU* 3.7 31.9 - - + -
385A FMT 4.1 16.6 - - - +
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Residues in contact with PRO 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 MSE 3.3 14.1 - - - +
127A ALA* 3.5 14.1 - - - +
129A LEU* 1.4 94.4 - - + +
131A TRP* 1.3 57.9 + - + +
133A GLU* 4.1 10.4 - - - +
134A SER* 3.0 32.4 + - - -
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Residues in contact with TRP 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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63A TRP* 4.1 4.0 - + - -
98A PHE* 3.4 72.2 - + + +
101A GLY* 4.4 2.7 - - - -
102A ALA* 3.5 45.5 - - + -
113A PHE* 3.9 15.7 - + + -
116A LEU* 4.0 4.9 - - + -
127A ALA 3.3 25.7 + - - -
128A TYR* 3.2 8.0 + - - +
129A LEU 3.2 0.4 - - - -
130A PRO* 1.3 77.0 - - + +
132A LEU* 1.3 65.8 + - - +
134A SER* 4.8 1.1 - - - -
135A TRP* 3.1 52.5 + + - +
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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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113A PHE* 3.9 14.1 - - + +
116A LEU* 3.8 20.2 - - + +
117A ALA* 3.8 25.1 - - + +
120A PHE* 3.8 44.0 - - + -
128A TYR* 3.2 13.0 + - + +
129A LEU* 3.1 11.5 + - + +
131A TRP* 1.3 79.6 - - - +
133A GLU* 1.3 63.2 + - - +
135A TRP* 4.2 0.6 - - - -
136A ALA* 3.1 27.5 + - - +
179A ILE* 4.0 28.2 - - + +
182A LEU* 4.6 5.2 - - + -
183A LEU* 4.6 6.7 - - + -
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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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129A LEU* 2.9 44.5 + - + +
130A PRO* 4.1 9.7 - - - +
132A LEU* 1.3 76.5 - - - +
134A SER* 1.3 58.9 + - - +
136A ALA* 4.1 1.5 - - - +
137A GLU* 3.0 38.4 + - + +
183A LEU* 4.0 14.3 - - + +
185A ARG* 3.5 37.7 + - - +
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Residues in contact with SER 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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105A LYS* 3.4 20.5 + - - -
130A PRO 3.0 19.5 + - - -
131A TRP* 4.0 2.9 - - - -
133A GLU* 1.3 79.0 - - - +
135A TRP* 1.3 61.3 + - - +
137A GLU* 3.5 4.8 + - - +
138A TRP* 3.0 27.2 + - - +
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Residues in contact with TRP 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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63A TRP* 3.8 18.4 - + - -
102A ALA* 4.8 3.8 - - + +
103A THR* 3.6 17.3 - - + -
104A THR 3.7 4.7 - - - -
105A LYS* 3.6 51.8 - - + +
106A ASN 4.5 0.7 - - - -
109A THR* 3.4 47.3 - - - -
110A MSE 3.7 33.9 - - + +
113A PHE* 3.2 38.7 - + + -
131A TRP* 3.1 40.5 + + - +
132A LEU 4.4 1.3 - - - +
134A SER* 1.3 80.2 + - - +
136A ALA* 1.3 64.2 + - - +
138A TRP* 3.3 4.3 + + - +
139A ALA 3.1 17.5 + - - -
179A ILE* 5.7 0.4 - - + -
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Residues in contact with ALA 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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110A MSE 4.1 10.6 - - - +
132A LEU 3.1 20.5 + - - +
133A GLU* 4.1 1.1 - - - +
135A TRP* 1.3 75.7 - - - +
137A GLU* 1.3 58.5 + - - +
139A ALA* 3.1 4.0 + - - +
140A MSE 3.0 31.0 + - - +
176A LEU* 3.9 7.9 - - + +
179A ILE* 3.8 16.4 - - + +
188A TYR* 3.4 33.7 - - + +
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Residues in contact with GLU 137 (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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133A GLU* 3.0 27.3 + - + +
134A SER* 3.8 5.2 - - - +
136A ALA* 1.3 76.2 - - - +
138A TRP* 1.3 57.5 + - - +
140A MSE 3.3 2.2 + - - -
141A HIS* 2.9 57.0 + - + +
142A GLU* 5.0 0.2 - - - +
185A ARG* 4.1 8.0 + - - +
188A TYR* 2.4 35.2 + - - +
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Residues in contact with TRP 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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105A LYS* 3.4 49.0 + - + +
106A ASN* 3.5 47.1 - - - -
107A VAL 4.0 1.3 - - - -
110A MSE 4.2 18.6 - - + -
134A SER 3.0 10.0 + - - +
135A TRP* 3.5 12.1 - + - +
136A ALA 3.2 0.2 - - - -
137A GLU* 1.3 76.8 - - - +
139A ALA* 1.3 84.1 + - + +
142A GLU* 2.8 66.1 + - + +
143A MSE 2.9 51.3 + - + +
144A PRO* 5.3 0.4 - - - +
154A MSE 4.0 10.8 - - + +
172A THR* 4.7 1.3 - - + -
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Residues in contact with ALA 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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110A MSE 4.1 16.4 - - + -
135A TRP 3.1 13.7 + - - +
136A ALA 3.1 8.0 + - - +
138A TRP* 1.3 91.6 - - + +
140A MSE 1.3 56.8 + - - +
143A MSE 4.1 4.9 - - - -
145A ARG* 2.9 31.5 + - - -
151A MSE 3.7 6.4 - - + +
172A THR* 4.2 13.9 - - + -
176A LEU* 4.4 13.7 - - + -
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Residues in contact with MSE 140 (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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136A ALA 3.0 14.4 + - - +
137A GLU* 3.6 1.3 - - - +
138A TRP 3.2 0.2 - - - -
139A ALA* 1.3 78.5 - - - +
141A HIS* 1.3 91.4 + - + +
145A ARG* 3.3 18.2 + - - +
176A LEU* 4.1 7.0 - - + -
187A GLN* 3.8 29.4 - - + +
188A TYR* 3.4 39.5 - - + -
191A GLU* 3.5 31.0 - - + +
383A FMT 4.0 14.4 - - - +
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Residues in contact with HIS 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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137A GLU* 2.9 41.6 + - + +
140A MSE 1.3 114.9 + - + +
142A GLU* 1.3 61.9 + - + +
143A MSE 3.9 2.6 - - - +
145A ARG* 5.1 0.4 - - - -
188A TYR* 5.6 0.4 - - - -
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Residues in contact with GLU 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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105A LYS* 5.7 1.9 + - - +
137A GLU 5.0 0.2 - - - +
138A TRP* 2.8 37.2 + - + +
141A HIS* 1.3 80.5 - - + +
143A MSE 1.3 70.7 + - - +
144A PRO* 3.3 5.9 - - - +
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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