Contacts of the helix formed by residues 117 - 136 (chain A) in PDB entry 2FD5
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 PRO 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ASP* 3.4 34.5 - - + +
56A LEU* 5.8 4.5 - - + -
113A VAL 4.8 0.3 - - - +
115A ARG 4.7 0.2 - - - +
116A LEU* 1.4 99.2 - - + +
118A GLU* 1.3 67.7 + - - +
119A GLY* 3.0 6.2 + - - +
120A PHE* 3.1 29.2 + - + +
121A ARG* 4.3 0.9 + - - +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU 3.5 3.5 + - - +
117A PRO* 1.3 71.9 - - - +
119A GLY* 1.3 62.7 + - - +
120A PHE 3.1 0.9 + - - -
121A ARG* 3.1 41.3 + - - +
122A GLU* 3.0 43.6 + - + +
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Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.6 25.4 - - - -
60A GLU* 5.7 0.2 - - - -
117A PRO* 3.0 5.0 + - - +
118A GLU* 1.3 78.2 - - - +
120A PHE* 1.3 55.0 + - - +
122A GLU* 3.7 13.9 + - - +
123A VAL* 2.9 36.7 + - - +
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Residues in contact with PHE 120 (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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20A LEU* 5.0 0.4 - - + -
25A ALA* 4.1 20.9 - - + -
52A ASP* 4.3 6.7 - - + -
55A MET* 3.8 8.1 - - + -
56A LEU* 3.5 39.0 - - + -
59A PHE* 3.6 52.1 - + + -
109A THR* 5.9 0.9 - - - -
113A VAL* 4.2 13.9 - - + +
116A LEU* 3.7 34.3 - - + -
117A PRO* 3.1 37.3 + - + +
119A GLY* 1.3 76.7 - - - +
121A ARG* 1.3 57.6 + - - +
124A LEU* 2.9 30.1 + - - +
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Residues in contact with ARG 121 (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 VAL* 3.7 24.5 + - + +
114A ALA* 3.5 39.4 + - - +
117A PRO 4.3 0.8 + - - +
118A GLU* 3.1 38.5 + - - +
120A PHE* 1.3 77.8 - - - +
122A GLU* 1.3 56.3 + - - +
124A LEU* 3.6 5.1 - - + +
125A SER* 2.7 46.3 + - - +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 3.0 42.8 + - + +
119A GLY* 3.7 13.3 - - - +
120A PHE 3.3 0.2 - - - -
121A ARG* 1.3 77.3 - - + +
123A VAL* 1.3 63.8 + - + +
125A SER* 3.3 5.2 + - - -
126A ARG* 3.2 40.9 + - - +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 4.4 0.9 - - + -
59A PHE* 4.1 7.0 - - + -
60A GLU* 3.4 47.6 - - + +
63A LEU* 3.6 26.5 - - + -
67A ARG* 5.2 4.2 + - - +
119A GLY* 2.9 21.1 + - - +
120A PHE 3.9 2.9 - - - +
122A GLU* 1.3 75.1 - - + +
124A LEU* 1.3 58.8 + - - +
126A ARG* 3.4 23.6 + - - +
127A HIS* 2.9 28.7 + - + +
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Residues in contact with LEU 124 (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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59A PHE* 4.4 7.8 - - + -
63A LEU* 4.8 1.1 - - - -
106A LEU* 3.7 37.9 - - + -
110A LEU* 3.8 23.3 - - + -
113A VAL* 4.3 22.2 - - + -
120A PHE 2.9 18.7 + - - +
121A ARG* 3.6 7.0 - - + +
123A VAL* 1.3 77.8 - - - +
125A SER* 1.3 57.9 + - - +
127A HIS* 3.2 7.1 + - + +
128A VAL* 2.9 43.4 + - + +
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Residues in contact with SER 125 (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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121A ARG* 2.7 31.2 + - - +
122A GLU* 3.8 5.5 - - - -
124A LEU* 1.3 78.9 - - - +
126A ARG* 1.3 64.1 + - - +
128A VAL* 3.4 6.2 + - - +
129A GLU* 3.0 36.2 + - - +
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Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 5.8 4.7 - - - +
122A GLU* 3.2 26.3 + - - +
123A VAL* 3.7 29.5 - - - +
125A SER* 1.3 79.6 - - - +
127A HIS* 1.3 58.5 + - - +
129A GLU* 3.2 13.9 + - - +
130A ILE* 2.9 54.2 + - + +
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Residues in contact with HIS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.4 51.2 - - + +
66A ARG* 4.2 8.7 - - + +
67A ARG* 2.9 47.7 + - + +
104A CYS* 5.4 2.2 - - - -
106A LEU* 4.1 18.6 - - + +
123A VAL 2.9 17.6 + - - +
124A LEU* 3.4 9.0 - - + +
126A ARG* 1.3 77.1 - - - +
128A VAL* 1.3 66.0 + - + +
130A ILE* 3.9 1.0 - - - +
131A MET* 2.9 53.1 + - + +
149A LEU* 6.4 0.4 - - + -
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Residues in contact with VAL 128 (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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106A LEU* 5.5 3.1 - - + -
124A LEU* 2.9 38.1 + - + +
125A SER* 3.8 6.5 - - - +
127A HIS* 1.3 80.0 - - + +
129A GLU* 1.3 64.8 + - + +
131A MET* 3.8 4.8 - - - +
132A VAL* 2.9 27.5 + - + +
146A LEU* 3.8 28.9 - - + -
149A LEU* 4.7 8.1 - - + -
153A ILE* 5.9 4.7 - - + -
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Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A SER* 3.0 28.4 + - - +
126A ARG* 3.6 13.9 - - - +
128A VAL* 1.3 77.9 - - + +
130A ILE* 1.3 63.6 + - + +
132A VAL* 4.0 3.7 - - - +
133A THR* 2.8 32.5 + - - +
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Residues in contact with ILE 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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67A ARG* 3.8 36.3 - - + +
126A ARG* 2.9 42.5 + - + +
127A HIS 3.9 2.9 - - - +
129A GLU* 1.3 76.1 - - + +
131A MET* 1.3 66.0 + - + +
133A THR* 3.4 6.4 + - - -
134A SER* 3.0 25.9 + - - +
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Residues in contact with MET 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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66A ARG* 4.5 5.8 - - - +
67A ARG* 4.0 21.8 - - + -
70A LEU* 3.3 42.6 - - + -
127A HIS* 2.9 59.4 + - + +
128A VAL* 3.8 3.1 - - - +
130A ILE* 1.3 77.2 - - + +
132A VAL* 1.3 63.6 + - - +
134A SER* 2.8 19.4 + - - +
135A LEU* 3.0 17.8 + - + +
149A LEU* 4.0 28.3 - - + -
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Residues in contact with VAL 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 VAL* 2.9 22.7 + - + +
129A GLU* 4.0 3.8 - - - +
131A MET* 1.3 76.0 - - - +
133A THR* 1.3 67.1 + - - +
135A LEU* 3.0 2.6 + - - +
136A ALA* 2.9 24.2 + - + +
142A THR* 3.7 41.7 - - + +
145A ALA* 4.1 8.7 - - + +
146A LEU* 3.6 31.2 - - + +
149A LEU* 3.6 22.2 - - + -
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Residues in contact with THR 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 GLU* 2.8 24.8 + - - +
130A ILE* 3.7 6.1 - - - -
132A VAL* 1.3 78.0 - - - +
134A SER* 1.3 61.7 + - - +
136A ALA* 3.3 20.9 - - - +
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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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70A LEU* 3.1 24.6 - - - +
82A ARG* 2.8 27.7 + - - -
130A ILE* 3.0 17.5 + - - +
131A MET* 2.8 18.5 + - - +
133A THR* 1.3 78.7 - - - +
135A LEU* 1.3 56.5 + - - +
136A ALA 4.8 0.6 - - - +
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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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70A LEU* 4.0 37.9 - - + -
73A LEU* 5.3 0.4 - - + -
79A GLY* 3.9 5.4 - - - -
82A ARG* 4.2 28.3 - - + +
83A ARG* 2.8 50.4 + - + +
86A ALA* 4.4 1.1 - - + -
131A MET* 3.0 22.1 + - + +
132A VAL 3.0 5.1 + - - +
134A SER* 1.3 78.8 - - - +
136A ALA* 1.3 58.8 + - - +
137A GLU 4.1 0.2 - - - -
145A ALA* 4.0 13.0 - - + +
148A ASP* 6.1 0.4 - - + -
149A LEU* 4.6 24.0 - - + -
152A MET* 4.8 11.7 - - + -
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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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82A ARG* 5.5 0.2 + - - -
83A ARG* 4.2 0.2 - - - +
132A VAL* 2.9 15.4 + - + +
133A THR* 3.3 15.2 - - - +
134A SER 3.5 1.3 - - - +
135A LEU* 1.3 79.5 - - - +
137A GLU* 1.3 65.5 + - - +
138A SER 3.4 5.3 + - - +
141A GLU* 3.7 34.5 - - + +
142A THR* 3.8 13.7 - - - +
145A ALA* 4.4 1.3 - - + -
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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
------------------------------------------------------------
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