Contacts of the helix formed by residues 129 - 142 (chain A) in PDB entry 6M85
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A TRP* 3.4 12.1 - - - -
111A LEU* 3.5 9.4 - - - +
127A VAL* 3.8 3.1 - - - +
128A ASN* 1.3 83.6 + - - +
130A PHE* 1.3 60.8 + - - -
131A VAL* 3.5 2.5 - - - -
132A ALA* 4.1 2.0 - - - +
133A ALA* 3.1 25.1 + - - +
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Residues in contact with PHE 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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95A LEU* 4.3 30.7 - - + -
98A GLY 4.4 2.7 - - - -
99A LEU* 3.9 40.2 - - + -
102A TRP* 3.6 32.5 - + + +
129A GLY* 1.3 71.0 - - - -
131A VAL* 1.3 61.9 + - + +
133A ALA* 3.1 2.2 + - - +
134A PHE* 2.7 47.2 + + + +
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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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129A GLY* 3.5 0.6 - - - -
130A PHE* 1.3 82.3 - - + +
132A ALA* 1.3 57.3 + - - +
134A PHE* 3.3 11.8 + - + +
135A LEU* 2.8 51.7 + - + +
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Residues in contact with ALA 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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126A GLN 3.6 20.4 - - - +
127A VAL* 3.9 3.3 - - - +
128A ASN* 3.2 35.3 + - - +
129A GLY* 3.8 3.4 + - - +
130A PHE 3.3 0.2 - - - -
131A VAL* 1.3 76.7 - - - +
133A ALA* 1.3 59.8 + - - +
135A LEU* 3.3 11.3 + - + -
136A PHE* 2.9 26.7 + - - +
149A ARG* 3.3 15.2 - - - +
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Residues in contact with ALA 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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98A GLY* 3.3 27.0 - - - +
101A PHE* 4.6 3.8 - - - +
102A TRP* 3.6 22.2 - - + +
127A VAL* 3.9 15.6 - - + +
129A GLY 3.1 16.1 + - - +
130A PHE* 3.1 8.4 + - - +
132A ALA* 1.3 75.6 - - - +
134A PHE* 1.3 61.7 + - - +
136A PHE* 3.4 5.5 + - - +
137A SER* 3.1 22.3 + - - -
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Residues in contact with PHE 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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91A LEU* 4.6 16.2 - - + -
94A TRP* 3.6 36.6 - + + -
95A LEU* 3.5 34.1 - - + -
98A GLY* 4.2 6.9 - - - -
130A PHE* 2.7 31.0 + + + +
131A VAL* 3.4 12.3 - - + +
133A ALA* 1.3 70.7 - - - +
135A LEU* 1.3 68.1 + - + +
137A SER* 3.1 4.5 + - - -
138A ILE* 3.0 49.4 + - + +
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Residues in contact with LEU 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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131A VAL* 2.8 43.4 + - + +
132A ALA* 3.6 5.2 - - - +
134A PHE* 1.3 79.7 - - + +
136A PHE* 1.3 56.8 + - - +
138A ILE* 3.4 15.5 + - + +
139A GLU* 2.8 51.0 + - - +
146A TYR* 6.4 1.1 - - + -
149A ARG* 3.6 29.6 - - - +
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Residues in contact with PHE 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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101A PHE* 3.6 49.6 - + + -
124A VAL* 3.7 25.6 - - + -
127A VAL* 4.5 6.3 - - + -
132A ALA 2.9 17.1 + - - +
133A ALA 3.7 4.5 - - - +
134A PHE 3.3 0.2 - - - -
135A LEU* 1.3 76.9 - - - +
137A SER* 1.3 54.9 + - - +
139A GLU* 3.9 10.5 - - + +
140A THR* 2.7 54.9 + - + -
149A ARG* 3.9 24.2 - - + +
150A CYS* 4.0 4.5 - - - -
151A VAL* 3.7 35.7 - - + -
162A VAL* 4.1 6.1 - - + -
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Residues in contact with SER 137 (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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94A TRP* 2.9 30.4 + - - -
97A PHE* 3.3 7.5 - - - +
98A GLY* 3.5 14.4 - - - -
101A PHE* 4.6 1.6 - - - -
133A ALA 3.1 11.1 + - - -
134A PHE 3.1 6.9 + - - -
136A PHE* 1.3 76.7 - - - +
138A ILE* 1.3 64.6 + - - +
140A THR 3.2 1.0 + - - -
141A GLN* 3.0 21.0 + - - +
165A GLN* 2.7 40.2 + - - +
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Residues in contact with ILE 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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94A TRP* 3.9 41.1 - - + -
134A PHE* 3.0 48.5 + - + +
135A LEU* 3.7 17.5 - - + +
137A SER* 1.3 73.6 + - - +
139A GLU* 1.3 58.2 + - + +
140A THR 3.2 0.3 + - - -
142A THR* 2.6 58.1 + - + +
144A ILE* 4.8 8.3 - - + -
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Residues in contact with GLU 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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135A LEU* 2.8 33.7 + - + +
136A PHE* 3.9 6.5 - - + +
138A ILE* 1.3 76.9 - - + +
140A THR* 1.3 57.1 + - - +
142A THR* 3.7 4.5 - - - -
143A THR* 3.2 5.2 + - - -
144A ILE* 2.9 15.5 + - + -
145A GLY* 2.9 36.1 + - - +
146A TYR* 3.5 42.6 + - + +
147A GLY 4.4 3.6 + - - -
149A ARG* 3.0 50.3 + - - +
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Residues in contact with THR 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 PHE* 2.7 45.2 + - - -
137A SER 3.7 0.2 - - - -
138A ILE 3.1 0.2 - - - -
139A GLU* 1.3 77.7 - - - +
141A GLN* 1.3 62.1 + - - +
143A THR* 3.2 17.9 + - - +
145A GLY* 5.6 0.4 - - - -
162A VAL* 4.0 30.1 - - + -
165A GLN* 3.6 28.5 - - + +
166A SER* 4.6 11.8 + - - +
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Residues in contact with GLN 141 (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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90A PHE* 4.4 9.5 - - + -
93A SER* 3.0 38.8 + - - +
94A TRP* 3.5 21.4 - - - +
97A PHE* 4.1 2.9 - - - -
137A SER 3.0 15.5 + - - +
140A THR* 1.3 73.2 - - - +
142A THR* 1.3 63.5 + - - +
143A THR* 2.9 15.3 + - - +
165A GLN* 3.1 36.7 + - + +
166A SER* 5.7 1.9 - - - +
168A VAL* 4.9 1.3 - - - -
169A GLY* 3.7 29.7 - - - -
172A ILE* 3.8 14.7 - - - +
173A ASP* 5.5 3.3 - - - +
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Residues in contact with THR 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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94A TRP* 3.6 31.6 - - + -
138A ILE* 2.6 35.0 + - + +
141A GLN* 1.3 75.2 - - - +
143A THR* 1.3 71.1 + - - +
144A ILE* 3.0 36.3 + - + +
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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