Contacts of the helix formed by residues 118 - 132 (chain A) in PDB entry 5OO2
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 VAL 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A TRP* 3.5 48.7 - - + +
45A ALA* 3.6 21.4 - - + +
46A PHE* 4.3 11.4 - - + -
49A ILE* 5.5 2.2 - - + +
116A PRO* 3.1 2.8 + - + +
117A PRO* 1.3 71.6 - - - +
119A HIS* 1.3 65.4 + - - +
120A ALA 3.3 1.1 - - - -
121A ILE* 3.0 31.2 + - + +
122A ALA 3.3 4.2 + - - -
258A ILE* 3.8 22.2 - - + -
387A LEU* 4.3 22.0 - - + -
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Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 2.8 42.4 + - - -
45A ALA* 4.0 16.1 - - + +
63A LEU* 4.6 9.7 - - + +
66A LEU* 3.3 25.0 - - + +
67A LEU* 6.3 0.4 - - + -
76A ILE* 4.2 9.2 - - + -
116A PRO 3.6 19.3 - - - -
117A PRO* 3.1 4.2 - - - +
118A VAL* 1.3 78.7 - - + +
120A ALA* 1.3 62.3 + - - +
122A ALA* 3.1 6.8 + - - +
123A VAL* 3.0 25.3 + - + +
152A LEU* 4.6 15.3 - - + -
155A TRP* 3.3 36.2 + + + +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO 4.4 1.8 + - - -
118A VAL 3.3 1.0 - - - -
119A HIS* 1.3 77.5 - - - +
121A ILE* 1.3 56.2 + - - +
123A VAL* 3.2 10.8 + - - +
124A GLN 3.0 23.0 + - - -
152A LEU* 5.4 2.8 - - + +
156A HIS* 4.3 7.6 + - - +
262A ALA* 3.5 37.0 - - + +
265A VAL* 3.5 14.0 - - + +
266A LEU* 4.0 24.2 - - + -
269A ILE* 4.0 1.2 - - - +
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Residues in contact with ILE 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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49A ILE* 4.3 3.8 - - + -
118A VAL* 3.0 23.7 + - + +
120A ALA* 1.3 74.8 - - - +
122A ALA* 1.3 64.3 + - - +
124A GLN* 3.2 4.8 + - - +
125A ARG* 3.0 22.4 + - + +
258A ILE* 5.4 5.2 - - + -
261A VAL* 4.3 12.8 - - + -
262A ALA* 5.0 8.3 - - - +
265A VAL* 4.4 12.6 - - + -
386A TRP* 3.9 22.9 - - + -
387A LEU* 4.3 19.5 - - + -
390A TRP* 3.7 51.8 - - + +
391A CYS* 5.1 0.9 - - - -
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Residues in contact with ALA 122 (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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45A ALA* 3.3 39.5 - - + +
48A ALA* 4.3 11.2 - - + -
49A ILE* 3.5 16.4 - - + +
63A LEU* 4.3 6.1 - - + -
118A VAL 3.3 2.4 + - - -
119A HIS* 3.1 9.5 + - - +
121A ILE* 1.3 79.1 - - - +
123A VAL* 1.3 56.2 + - - +
125A ARG* 3.2 3.3 + - - +
126A ILE* 2.9 34.1 + - - +
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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
----------------------------------------------------------
63A LEU* 3.8 18.4 - - + -
119A HIS* 3.0 17.7 + - + +
120A ALA* 3.2 9.6 + - - +
122A ALA* 1.3 74.6 - - - +
124A GLN* 1.3 62.9 + - - +
126A ILE* 3.3 9.9 + - + +
127A LEU* 2.9 35.0 + - + +
144A PHE* 3.9 18.4 - - + -
145A LEU* 4.0 19.3 - - + -
152A LEU* 4.1 20.0 - - + -
266A LEU* 5.4 1.6 - - + -
269A ILE* 3.8 16.8 - - + -
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Residues in contact with GLN 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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120A ALA 3.0 13.2 + - - +
121A ILE* 3.2 8.5 + - - +
123A VAL* 1.3 77.2 - - - +
125A ARG* 1.3 56.7 + - - +
127A LEU* 3.2 5.7 + - + +
128A GLU* 2.9 59.2 + - + +
131A ARG* 5.6 2.5 - - - +
265A VAL* 3.3 35.4 - - + +
268A GLU* 4.8 3.4 - - - +
269A ILE* 3.9 12.0 - - + +
390A TRP* 3.7 23.5 - - + +
394A ARG* 4.3 9.3 + - - +
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Residues in contact with ARG 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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49A ILE* 4.1 33.4 - - + -
52A ALA* 4.6 1.8 - - + -
121A ILE 3.0 17.9 + - - +
122A ALA 3.2 5.8 + - - +
124A GLN* 1.3 75.1 - - + +
126A ILE* 1.3 62.3 + - - +
128A GLU* 2.9 30.7 + - - +
129A HIS* 2.9 45.4 + - + +
386A TRP* 4.6 3.1 - - + -
390A TRP* 3.8 26.6 - - - +
443A ASP* 2.8 35.5 + - - +
399B GLU* 4.3 2.8 + - - -
501B GOL 2.9 42.4 + - - -
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Residues in contact with ILE 126 (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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48A ALA* 4.1 13.7 - - + +
52A ALA* 4.1 9.4 - - + -
56A VAL* 4.2 18.0 - - + +
59A ALA* 3.8 36.1 - - + +
60A VAL* 4.1 22.9 - - + +
63A LEU* 3.7 29.4 - - + -
122A ALA 2.9 18.6 + - - +
123A VAL* 3.3 7.8 + - + +
125A ARG* 1.3 76.6 - - + +
127A LEU* 1.3 58.4 + - + +
129A HIS* 3.4 2.1 + - - +
130A ALA* 2.8 27.4 + - - +
141A ALA* 4.4 8.5 - - + -
144A PHE* 5.6 5.2 - - + -
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Residues in contact with LEU 127 (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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123A VAL* 2.9 31.6 + - + +
124A GLN* 3.7 4.7 - - + +
126A ILE* 1.3 78.1 - - + +
128A GLU* 1.3 58.4 + - - +
130A ALA* 3.1 4.5 + - + +
131A ARG* 2.9 49.6 + - - +
141A ALA* 3.8 26.9 - - + +
142A GLU* 4.9 0.4 - - + +
144A PHE* 6.5 0.4 - - + -
145A LEU* 4.1 13.2 - - + -
269A ILE* 3.9 37.7 - - + -
273A TYR* 3.7 31.4 - - + +
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Residues in contact with GLU 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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124A GLN* 2.9 49.1 + - + +
125A ARG* 2.9 39.9 + - - +
127A LEU* 1.3 73.7 - - - +
129A HIS* 1.3 66.9 + - - +
131A ARG* 3.5 28.1 + - - +
132A THR* 3.4 23.7 + - - +
390A TRP* 5.2 0.9 + - - -
399B GLU* 3.4 34.9 - - + +
501B GOL 3.9 8.0 - - - +
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Residues in contact with HIS 129 (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 ILE 4.9 1.6 - - - -
52A ALA* 3.6 25.4 - - + +
53A PRO* 3.4 44.4 - - + +
56A VAL* 4.5 3.6 - - + -
125A ARG* 2.9 55.0 + - + +
126A ILE 3.7 3.6 - - - +
128A GLU* 1.3 75.3 - - - +
130A ALA* 1.3 64.4 + - - +
132A THR* 2.9 23.0 + - - -
133A ARG* 3.3 15.5 - - + +
443A ASP* 4.8 4.3 - - - -
446A GLY* 6.2 1.0 - - - -
501B GOL 3.6 33.4 + - - -
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Residues in contact with ALA 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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56A VAL* 4.2 5.4 - - + -
126A ILE 2.8 18.6 + - - +
127A LEU* 3.1 4.0 + - - +
129A HIS* 1.3 76.0 - - - +
131A ARG* 1.3 62.5 + - + +
133A ARG* 3.0 13.0 + - - +
134A GLY 3.8 5.0 + - - +
137A THR* 3.9 27.4 - - + +
138A ARG* 3.3 18.4 + - + +
141A ALA* 3.7 26.5 - - + -
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Residues in contact with ARG 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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124A GLN* 5.6 2.6 - - - +
127A LEU* 2.9 32.7 + - + +
128A GLU* 3.6 33.4 + - - +
129A HIS 3.3 0.4 - - - -
130A ALA* 1.3 75.5 - - + +
132A THR* 1.3 61.9 + - + +
138A ARG* 3.2 38.8 + - + +
272A ASP* 4.7 8.8 + - - -
273A TYR* 2.8 46.4 + - - +
502A GOL 3.5 31.6 + - - -
399B GLU* 5.8 1.4 - - - +
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Residues in contact with THR 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 GLU 3.4 15.0 - - - +
129A HIS* 2.9 16.6 + - - -
131A ARG* 1.3 79.2 - - + +
133A ARG* 1.3 77.9 + - - +
134A GLY 3.6 1.1 + - - -
399B GLU* 4.0 15.9 - - - +
402B ARG* 4.0 13.2 - - - +
403B LEU* 4.2 15.3 - - + -
501B GOL 4.5 10.9 - - - -
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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
------------------------------------------------------------
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