Contacts of the helix formed by residues 154 - 165 (chain A) in PDB entry 2FG5
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 ASN 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A VAL* 4.4 16.3 - - + +
146A GLU* 3.2 25.0 + - - +
147A THR* 3.5 7.8 - - + +
152A ALA 4.1 1.8 + - - -
153A ILE* 1.3 82.3 - - - +
155A ILE* 1.3 59.2 + - - +
156A GLU 3.5 1.1 - - - -
157A GLU* 3.2 43.8 + - + +
158A LEU* 3.0 26.2 + - - +
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Residues in contact with ILE 155 (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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21A ILE* 3.7 39.3 - - + +
24A ARG* 3.6 21.8 - - + -
25A PHE* 3.6 38.1 - - + +
147A THR* 3.7 26.0 - - + -
148A SER 4.0 7.9 - - - +
149A ALA* 4.1 11.9 - - - +
152A ALA* 4.5 2.4 - - + -
153A ILE 3.2 8.7 - - - +
154A ASN* 1.3 75.4 - - - +
156A GLU* 1.3 67.4 + - - +
157A GLU* 3.8 0.4 + - - -
158A LEU* 3.2 12.3 + - - +
159A PHE* 3.2 20.9 - - + -
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Residues in contact with GLU 156 (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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25A PHE* 3.6 19.5 - - - +
45A LYS* 3.2 35.6 + - - -
47A VAL* 3.8 12.4 - - + +
155A ILE* 1.3 78.5 - - - +
157A GLU* 1.3 66.9 + - - +
159A PHE* 3.1 6.8 + - - +
160A GLN* 2.9 46.2 + - + +
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Residues in contact with GLU 157 (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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143A ILE* 5.0 0.9 - - - +
145A VAL* 5.1 9.3 - - + +
154A ASN* 3.2 45.7 + - + +
155A ILE 3.2 0.5 + - - -
156A GLU* 1.3 82.7 + - - +
158A LEU* 1.3 59.7 + - - +
160A GLN* 3.6 22.0 - - - +
161A GLY* 2.9 26.9 + - - -
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Residues in contact with LEU 158 (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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21A ILE* 4.0 25.6 - - + -
82A VAL* 3.9 26.7 - - + -
114A ALA* 4.1 21.5 - - + -
115A ILE 4.2 3.6 - - - +
116A ALA* 4.1 20.9 - - + -
143A ILE* 4.1 4.9 - - + +
145A VAL* 3.7 26.6 - - + +
147A THR* 4.6 4.5 - - + -
154A ASN 3.0 15.5 + - - +
155A ILE* 3.4 9.2 - - - +
157A GLU* 1.3 75.8 - - - +
159A PHE* 1.3 70.7 + - + +
161A GLY* 3.3 10.1 + - - -
162A ILE* 3.5 14.4 + - - +
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Residues in contact with PHE 159 (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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8A VAL* 4.6 10.5 - - + -
10A LEU* 5.3 4.7 - - + -
21A ILE* 4.3 11.2 - - + -
22A VAL* 5.4 3.1 - - + -
25A PHE* 3.5 61.5 - + + -
47A VAL* 6.4 2.0 - - + -
56A PHE* 3.7 19.7 - + + -
58A ILE* 4.3 24.2 - - + -
82A VAL* 4.7 5.2 - - + -
155A ILE 3.2 21.5 - - - -
156A GLU 3.1 5.8 + - - +
158A LEU* 1.3 91.1 - - + +
160A GLN* 1.3 61.6 + - - +
161A GLY 3.0 1.6 - - - -
162A ILE* 3.2 26.8 + - + +
163A SER* 3.0 30.6 + - - -
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Residues in contact with GLN 160 (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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47A VAL* 5.6 10.9 - - + +
156A GLU* 2.9 36.4 + - + +
157A GLU* 3.2 26.1 + - - +
159A PHE* 1.3 76.5 - - - +
161A GLY* 1.3 56.8 + - - +
163A SER* 3.7 8.4 - - - -
164A ARG* 3.0 30.5 + - - +
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Residues in contact with GLY 161 (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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143A ILE* 3.4 29.6 - - - +
157A GLU 2.9 12.4 + - - -
158A LEU 3.3 1.5 + - - -
159A PHE 3.0 0.6 - - - -
160A GLN* 1.3 74.1 - - - +
162A ILE* 1.3 64.5 + - - +
164A ARG* 3.5 6.0 + - - +
165A GLN* 3.5 26.8 + - - +
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Residues in contact with ILE 162 (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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6A LEU* 4.9 1.8 - - + -
8A VAL* 4.3 10.8 - - + -
56A PHE* 3.8 16.8 - - + -
80A ALA* 3.7 27.1 - - + -
82A VAL* 3.7 30.1 - - + -
112A VAL* 4.4 11.3 - - + +
114A ALA* 4.2 14.4 - - + -
143A ILE* 4.4 0.2 - - - +
158A LEU 3.5 11.3 + - - +
159A PHE* 3.2 29.9 + - + +
161A GLY* 1.3 73.1 - - - +
163A SER* 1.3 65.3 + - - +
165A GLN* 3.2 13.7 + - - +
166A ILE* 3.7 24.8 - - + +
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Residues in contact with SER 163 (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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47A VAL* 4.9 4.7 - - - +
49A CYS* 3.5 29.6 - - - +
54A HIS* 3.1 35.1 + - - +
56A PHE* 3.3 18.5 - - - -
159A PHE 3.0 11.6 + - - -
160A GLN* 3.7 9.1 - - - -
162A ILE* 1.3 79.2 - - - +
164A ARG* 1.3 60.8 + - - +
165A GLN 3.3 0.9 + - - -
166A ILE* 3.4 16.7 + - - +
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Residues in contact with ARG 164 (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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49A CYS* 5.2 2.9 - - - -
160A GLN 3.0 19.6 + - - +
161A GLY* 3.8 7.0 - - - +
162A ILE 3.3 0.4 - - - -
163A SER* 1.3 75.9 - - - +
165A GLN* 1.3 58.7 + - + +
166A ILE 3.2 8.6 + - - +
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Residues in contact with GLN 165 (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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112A VAL* 3.3 36.9 - - + +
113A MET 4.4 2.7 + - - +
141A GLY 4.6 10.5 + - - +
142A ALA* 4.9 1.0 - - - +
143A ILE* 3.2 45.3 - - - +
161A GLY 3.5 9.6 + - - +
162A ILE 3.2 10.1 + - - +
164A ARG* 1.3 76.1 - - + +
166A ILE* 1.3 66.0 + - - +
167A PRO* 4.5 2.7 - - - +
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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