Contacts of the helix formed by residues 129 - 145 (chain A) in PDB entry 5FQU
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 LEU 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A PRO* 1.3 77.9 - - + +
130A GLY* 1.3 64.5 + - - +
131A VAL 3.2 1.3 - - - -
132A ILE* 4.0 4.8 - - - +
133A GLN* 3.3 33.0 + - - +
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Residues in contact with GLY 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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128A PRO 4.6 1.0 - - - -
129A LEU* 1.3 78.0 - - - +
131A VAL* 1.3 57.0 + - - +
133A GLN* 3.9 0.4 + - - -
134A GLY 3.2 15.4 + - - -
193A ALA 5.8 1.3 - - - -
194A VAL* 4.1 16.5 - - - +
195A PHE* 3.7 2.7 - - - -
196A ALA* 2.9 30.3 + - - -
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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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128A PRO* 3.9 22.2 - - + -
129A LEU 3.2 1.6 - - - +
130A GLY* 1.3 76.8 - - - +
132A ILE* 1.3 61.0 + - + +
134A GLY* 3.3 1.4 + - - +
135A GLN* 3.0 46.2 + - + +
196A ALA* 3.9 20.9 - - + -
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Residues in contact with ILE 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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128A PRO 3.3 22.2 + - - +
129A LEU* 3.6 6.8 + - - +
130A GLY 3.5 0.4 - - - -
131A VAL* 1.3 75.4 - - + +
133A GLN* 1.3 66.0 + - + +
135A GLN* 3.4 15.9 + - - +
136A ASN* 2.9 42.9 + - - +
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Residues in contact with GLN 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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88A GLN 5.9 1.0 + - - -
129A LEU* 3.3 19.2 + - + +
130A GLY 4.2 0.2 - - - +
132A ILE* 1.3 79.6 - - + +
134A GLY* 1.3 60.1 + - - +
136A ASN* 3.7 9.7 - - - +
137A LEU* 2.9 31.7 + - - +
194A VAL* 2.9 38.8 - - - +
195A PHE* 3.5 14.0 - - + -
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Residues in contact with GLY 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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130A GLY 3.2 15.7 + - - -
131A VAL* 3.6 5.2 - - - -
132A ILE 3.2 0.6 - - - -
133A GLN* 1.3 78.2 - - - +
135A GLN* 1.3 60.0 + - - +
137A LEU* 3.7 0.4 + - - -
138A ALA* 3.2 12.0 + - - +
186A ARG* 2.8 48.3 + - - -
195A PHE* 3.9 5.5 - - - -
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Residues in contact with GLN 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* 3.0 31.5 + - + +
132A ILE* 3.8 17.8 - - - +
133A GLN 3.3 0.2 - - - -
134A GLY* 1.3 72.4 - - - +
136A ASN* 1.3 66.2 + - - +
138A ALA* 2.9 18.2 + - - +
139A MSE 3.0 32.4 + - + +
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Residues in contact with ASN 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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132A ILE* 2.9 34.8 + - - +
133A GLN* 3.7 10.2 - - - +
135A GLN* 1.3 74.9 - - - +
137A LEU* 1.3 61.1 + - - +
139A MSE 3.3 22.7 + - - +
140A VAL* 3.1 30.7 + - + +
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Residues in contact with LEU 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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64A VAL* 5.6 2.2 - - + -
133A GLN 2.9 17.8 + - - +
134A GLY 4.0 2.9 - - - +
136A ASN* 1.3 74.6 - - - +
138A ALA* 1.3 57.9 + - - +
140A VAL* 3.4 7.8 + - + +
141A LEU* 3.0 56.0 + - + +
186A ARG* 4.1 15.9 - - - +
189A MSE 3.7 36.8 - - + -
195A PHE* 3.9 34.5 - - + -
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Residues in contact with ALA 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 GLY 3.2 14.7 + - - +
135A GLN* 2.9 13.0 + - - +
137A LEU* 1.3 78.1 - - - +
139A MSE 1.3 57.5 + - + +
141A LEU* 3.7 5.8 + - - +
142A GLU* 3.2 38.1 + - - +
182A PRO* 5.2 0.6 - - - +
186A ARG* 3.9 18.8 - - + +
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Residues in contact with MSE 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 GLN* 3.0 35.7 + - + +
136A ASN* 3.3 31.9 - - - +
138A ALA* 1.3 76.3 - - + +
140A VAL* 1.3 64.4 + - + +
142A GLU* 3.5 12.6 + - - +
143A SER* 2.9 29.0 + - - -
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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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85A MSE 5.2 24.5 - - + -
136A ASN* 3.1 19.0 + - + +
137A LEU* 3.8 9.0 - - + +
139A MSE 1.3 76.6 - - + +
141A LEU* 1.3 65.3 + - + +
143A SER* 3.0 9.1 + - - -
144A LEU* 3.0 43.3 + - + +
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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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64A VAL* 4.6 19.5 - - + -
68A LEU* 5.4 4.5 - - + -
137A LEU* 3.0 40.4 + - + +
138A ALA* 4.0 4.3 - - - +
139A MSE 3.4 0.2 - - - -
140A VAL* 1.3 77.7 - - + +
142A GLU* 1.3 56.9 + - - +
144A LEU* 3.7 13.3 + - + +
145A LEU* 3.1 41.1 + - + +
182A PRO* 3.9 15.4 - - + +
185A ILE* 3.8 22.2 - - + -
186A ARG* 3.7 39.9 - - + +
189A MSE 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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138A ALA* 3.2 26.1 + - - +
139A MSE 4.0 13.5 - - - +
140A VAL 3.1 1.2 - - - -
141A LEU* 1.3 76.4 - - - +
143A SER* 1.3 58.0 + - - +
145A LEU 3.3 0.7 + - - -
146A VAL* 3.0 30.5 + - - +
182A PRO* 3.7 25.5 - - + +
183A GLN* 5.7 2.4 + - - +
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Residues in contact with SER 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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139A MSE 2.9 14.8 + - - -
140A VAL* 3.0 11.1 + - - -
142A GLU* 1.3 75.3 - - - +
144A LEU* 1.3 68.1 + - - +
145A LEU 3.3 0.7 + - - -
146A VAL* 3.5 20.8 + - - +
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Residues in contact with LEU 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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68A LEU* 3.8 33.0 - - + -
73A TYR* 2.9 40.6 + - + +
81A ILE* 3.7 37.2 - - + -
85A MSE 6.5 0.2 - - - -
140A VAL* 3.0 40.3 + - + +
141A LEU* 4.1 10.3 - - + +
143A SER* 1.3 79.9 - - - +
145A LEU* 1.3 61.0 + - - +
146A VAL* 3.6 1.2 + - - +
147A HIS* 3.8 5.9 + - - -
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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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68A LEU* 3.9 22.7 - - + -
71A SER* 3.4 36.3 - - - +
141A LEU* 3.1 25.9 + - + +
142A GLU 3.6 2.7 - - - -
143A SER 3.2 0.2 - - - -
144A LEU* 1.3 82.5 - - - +
146A VAL* 1.3 53.4 + - - +
147A HIS* 3.0 6.7 - - + -
148A THR* 2.7 43.1 + - - +
149A SER* 4.1 0.3 + - - -
181A LEU* 4.1 16.6 - - + -
182A PRO* 4.0 33.8 - - + +
185A ILE* 4.3 11.7 - - + -
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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