Contacts of the helix formed by residues 134 - 146 (chain A) in PDB entry 3W7F
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 ALA 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A CYS 3.0 4.7 + - - +
131A TYR 3.4 0.4 + - - -
133A VAL* 1.3 80.6 - - - +
135A GLY* 1.3 66.1 + - - +
136A THR 3.1 1.8 - - - -
137A VAL* 3.2 11.5 + - - +
138A GLY 3.2 15.6 + - - -
161A GLY* 3.3 33.8 - - - +
165A GLN* 3.7 22.2 - - + +
302A FPS 3.9 19.6 - - + +
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Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A CYS 3.0 6.9 + - - -
131A TYR* 2.9 25.2 + - - -
134A ALA* 1.3 72.5 - - - +
136A THR* 1.3 56.2 + - - +
138A GLY* 3.2 3.3 + - - -
139A GLU* 3.0 29.6 + - - +
158A ARG* 3.5 28.3 - - - -
162A GLU* 3.8 8.8 - - - +
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Residues in contact with THR 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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103A SER* 3.5 27.2 - - - +
106A ASN* 3.6 13.2 - - + -
107A LEU* 3.8 8.7 - - - +
131A TYR* 3.0 41.3 + - + +
132A GLY 2.9 22.3 + - - +
133A VAL 4.0 4.7 - - - -
135A GLY* 1.3 75.1 - - - +
137A VAL* 1.3 61.5 + - - +
139A GLU* 3.3 11.7 + - - +
140A VAL* 2.9 31.5 + - - +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.9 1.6 - - + -
44A CYS* 4.3 22.2 - - - -
107A LEU* 4.6 4.5 - - + -
133A VAL 3.6 22.9 - - - +
134A ALA* 3.2 9.3 + - - +
136A THR* 1.3 76.1 + - - +
138A GLY* 1.3 61.5 + - - +
140A VAL* 3.2 11.3 + - + +
141A LEU* 2.8 44.2 + - + +
301A FPS 3.7 41.1 - - + -
302A FPS 4.1 10.1 - - + -
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Residues in contact with GLY 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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134A ALA 3.2 7.7 + - - -
135A GLY 3.2 8.2 + - - -
137A VAL* 1.3 77.2 - - - +
139A GLU* 1.3 61.9 + - - +
141A LEU* 3.1 2.5 + - - +
142A THR* 3.0 23.9 + - - -
157A ALA* 3.5 29.1 - - - +
302A FPS 3.9 19.8 - - - +
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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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100A ALA* 4.4 5.0 - - + +
103A SER* 2.4 35.4 + - - +
131A TYR* 2.9 35.0 + - - -
135A GLY 3.0 13.4 + - - +
136A THR* 3.5 4.1 - - - +
138A GLY* 1.3 76.1 - - - +
140A VAL* 1.3 65.0 + - - +
142A THR* 3.1 22.1 + - - -
143A PRO* 3.7 2.6 - - - +
154A TYR* 3.5 22.6 - - + +
157A ALA* 4.4 0.8 - - - +
158A ARG* 3.0 46.7 + - + +
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Residues in contact with VAL 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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40A ILE* 3.6 38.9 - - + +
44A CYS* 4.9 1.6 - - - -
99A ILE* 4.8 6.3 - - + +
100A ALA* 3.6 21.3 + - + +
103A SER* 3.5 26.9 - - - -
104A PHE* 4.2 32.1 - - + +
136A THR 2.9 14.3 + - - +
137A VAL* 3.2 19.7 - - + +
139A GLU* 1.3 72.3 - - - +
141A LEU* 1.3 65.4 + - - +
142A THR 3.2 0.9 + - - -
143A PRO* 3.5 14.6 - - - +
144A ILE* 4.4 0.9 - - - +
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Residues in contact with LEU 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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26A PHE* 4.9 2.9 - - + -
37A VAL* 4.1 25.4 - - + -
40A ILE* 4.0 30.1 - - + -
137A VAL* 2.8 29.8 + - + +
138A GLY* 3.7 4.5 - - - +
140A VAL* 1.3 73.9 - - - +
142A THR* 1.3 62.3 + - - +
143A PRO 3.5 0.4 - - - -
144A ILE* 3.0 19.7 + - + +
145A LEU* 3.3 23.7 + - + +
301A FPS 3.7 28.9 - - + -
302A FPS 4.0 35.0 - - + -
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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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138A GLY 3.0 16.0 + - - -
139A GLU 3.1 8.9 + - - -
141A LEU* 1.3 76.1 - - - +
143A PRO* 1.3 72.4 - - + +
144A ILE 2.9 2.3 + - - -
145A LEU* 3.3 3.1 + - - -
146A SER* 3.3 21.4 + - - -
149A GLU* 4.9 6.7 - - - -
153A THR* 3.4 32.1 - - + -
154A TYR* 3.5 32.6 - - + +
157A ALA* 3.2 18.6 - - - +
233A PHE* 5.3 2.9 - - - -
302A FPS 5.9 0.2 - - - -
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Residues in contact with PRO 143 (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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97A LYS* 3.1 27.6 + - + +
98A ASN* 3.3 47.6 - - - +
99A ILE* 4.8 3.1 - - + +
100A ALA 5.7 0.7 - - - +
139A GLU 3.7 5.4 - - - +
140A VAL* 3.5 14.1 - - - +
142A THR* 1.3 92.1 - - + +
144A ILE* 1.3 62.7 + - + +
146A SER 3.3 13.1 - - - +
149A GLU* 4.0 19.1 - - + +
154A TYR* 3.8 12.1 - - - +
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Residues in contact with ILE 144 (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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33A GLN* 3.6 52.0 + - + +
36A ALA* 3.9 21.8 - - + -
37A VAL* 4.4 4.9 - - + -
40A ILE* 3.7 28.9 - - + -
93A VAL* 4.2 5.2 - - + -
97A LYS* 3.7 40.7 + - + +
99A ILE* 4.8 2.7 - - + -
140A VAL 4.4 1.3 - - - +
141A LEU* 3.0 13.8 + - + +
143A PRO* 1.3 85.1 - - + +
145A LEU* 1.3 68.1 + - + +
146A SER 3.3 2.7 + - - +
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Residues in contact with LEU 145 (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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26A PHE* 4.5 9.6 - - + -
29A LEU* 4.2 25.6 - - + -
33A GLN* 4.5 2.2 - - - +
37A VAL* 4.4 5.4 - - + -
141A LEU* 3.3 26.3 + - + +
142A THR 3.3 1.8 + - - +
144A ILE* 1.3 90.2 - - + +
146A SER* 1.3 59.4 + - - +
233A PHE* 3.6 18.8 - - + +
234A SER* 2.8 29.2 + - - -
237A ALA* 3.8 16.7 - - + +
240A ILE* 6.4 0.2 - - + -
241A ILE* 3.9 16.6 - - + -
302A FPS 3.9 31.9 - - + -
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Residues in contact with SER 146 (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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97A LYS* 5.2 1.9 + - - -
142A THR* 3.3 12.5 + - - +
143A PRO* 3.3 21.3 - - - +
144A ILE 3.3 2.8 + - - -
145A LEU* 1.3 82.2 - - - +
147A ASP* 1.3 66.4 + - - +
148A HIS 3.0 20.6 + - - -
149A GLU* 4.6 4.9 - - - +
153A THR* 3.8 13.3 - - - +
232A VAL 2.8 26.2 + - - -
233A PHE* 4.1 3.6 - - - -
234A SER* 3.9 8.1 - - - +
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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