Contacts of the helix formed by residues 120 - 139 (chain Z) in PDB entry 6F0X
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 SER 120 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8Z GLU* 5.5 3.6 - - - -
119Z LYS* 1.3 77.5 - - - +
121Z GLN* 1.3 65.3 + - - +
122Z LYS* 3.2 16.0 - - - +
123Z ALA* 2.5 35.3 + - - +
124Z ILE* 3.0 29.0 + - - +
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Residues in contact with GLN 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Z GLN* 4.9 14.8 - - - +
10Z GLY 5.1 6.8 - - - +
11Z ILE* 5.1 5.0 - - - +
19Z ILE* 3.7 29.9 - - - +
119Z LYS 4.1 0.6 + - - +
120Z SER* 1.3 70.1 - - - +
122Z LYS* 1.3 61.5 + - - +
124Z ILE* 4.6 11.8 - - - +
125Z GLN* 2.8 39.4 + - - +
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Residues in contact with LYS 122 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203P LEU* 5.2 6.7 + - - +
204P GLN* 3.7 27.3 + - - +
120Z SER* 3.2 12.9 - - - +
121Z GLN* 1.3 78.1 - - - +
123Z ALA* 1.3 66.3 + - + +
125Z GLN* 3.6 7.0 - - - +
126Z ASP* 2.9 58.3 + - - +
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Residues in contact with ALA 123 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119Z LYS* 4.4 10.8 - - + -
120Z SER* 2.5 30.5 + - - +
122Z LYS* 1.3 82.6 - - + +
124Z ILE* 1.3 63.7 + - - +
126Z ASP* 3.3 2.7 + - - +
127Z GLU* 2.9 40.8 + - - +
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Residues in contact with ILE 124 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Z ILE* 4.6 16.4 - - + -
19Z ILE* 4.5 21.3 - - + -
20Z VAL* 6.1 0.4 - - + -
119Z LYS* 3.9 32.1 - - + -
120Z SER 3.0 17.9 + - - +
121Z GLN* 4.3 15.9 - - - +
123Z ALA* 1.3 73.7 - - - +
125Z GLN* 1.3 58.2 + - - +
127Z GLU* 3.2 9.6 + - - +
128Z ILE* 2.9 45.9 + - + +
187Z THR 4.5 11.0 - - - +
188Z THR* 4.8 19.3 - - + +
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Residues in contact with GLN 125 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49Z TYR* 3.0 56.0 + - + +
50Z GLY* 3.2 8.3 - - - +
121Z GLN* 2.8 28.2 + - - +
122Z LYS* 3.6 5.5 - - - +
124Z ILE* 1.3 78.6 - - - +
126Z ASP* 1.3 59.7 + - - +
128Z ILE* 3.2 4.8 + - - +
129Z ARG* 2.9 32.7 + - - +
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Residues in contact with ASP 126 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203P LEU* 3.2 33.8 - - + +
204P GLN* 5.8 0.2 + - - -
205P ALA* 3.8 8.3 + - - +
122Z LYS* 2.9 48.7 + - - +
123Z ALA* 4.0 3.1 - - - +
125Z GLN* 1.3 79.9 - - - +
127Z GLU* 1.3 59.0 + - - +
129Z ARG* 2.2 43.8 + - - +
130Z SER* 2.9 25.6 + - - -
133Z ARG* 4.6 1.7 + - - -
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Residues in contact with GLU 127 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203P LEU* 3.5 40.9 - - + +
119Z LYS* 4.2 13.0 + - - -
123Z ALA* 2.9 31.7 + - - +
124Z ILE* 3.7 5.1 - - - +
126Z ASP* 1.3 74.8 - - - +
128Z ILE* 1.3 60.7 + - + +
130Z SER* 3.1 5.7 - - - -
131Z VAL* 3.0 30.2 + - - +
185Z SER 5.5 1.5 - - - +
186Z PHE* 4.6 13.1 - - + +
187Z THR* 4.2 23.7 + - - +
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Residues in contact with ILE 128 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Z ILE* 4.1 18.4 - - + -
20Z VAL* 5.2 4.5 - - + -
23Z PHE* 3.4 43.3 - - + -
49Z TYR* 3.4 36.8 - - + -
124Z ILE* 2.9 28.0 + - + +
125Z GLN 3.7 3.1 - - - +
127Z GLU* 1.3 77.0 - - + +
129Z ARG* 1.3 56.7 + - - +
131Z VAL* 3.0 6.9 + - - +
132Z ILE* 2.8 37.6 + - + +
186Z PHE* 4.4 14.4 - - + -
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Residues in contact with ARG 129 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85P GLN* 3.3 29.9 - - - +
205P ALA* 3.6 12.7 - - - +
49Z TYR* 2.2 32.4 + - - +
50Z GLY* 3.1 21.1 + - - -
51Z LEU* 3.2 32.2 - - + +
125Z GLN* 2.9 18.8 + - - +
126Z ASP* 2.2 46.9 + - - +
128Z ILE* 1.3 77.2 - - - +
130Z SER* 1.3 61.9 + - - +
132Z ILE* 3.2 2.6 + - - +
133Z ARG* 2.9 49.3 + - - +
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Residues in contact with SER 130 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200P PHE 5.1 1.7 + - - -
201P SER* 5.7 1.0 - - - -
202P GLU 5.8 1.1 + - - -
203P LEU* 3.8 19.5 - - - +
126Z ASP 2.9 12.3 + - - -
127Z GLU 3.1 11.0 + - - -
129Z ARG* 1.3 75.4 - - - +
131Z VAL* 1.3 63.7 + - - +
133Z ARG* 3.2 22.8 + - - +
134Z GLN* 2.9 26.7 + - - +
184Z ARG* 3.5 30.7 + - - +
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Residues in contact with VAL 131 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Z PHE* 3.4 31.2 - - + -
127Z GLU 3.0 15.1 + - - +
128Z ILE* 3.0 10.9 + - - +
130Z SER* 1.3 77.9 - - - +
132Z ILE* 1.3 58.0 + - + +
134Z GLN* 3.2 11.2 + - - +
135Z ILE* 2.9 50.7 + - + +
183Z LEU* 5.9 1.8 - - + -
184Z ARG* 4.8 9.0 - - + +
185Z SER 4.8 2.0 - - - +
186Z PHE* 3.4 39.7 - - + -
195Z SER* 5.6 3.4 - - - +
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Residues in contact with ILE 132 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82P TYR* 5.0 5.2 - - - +
23Z PHE* 5.1 5.8 - - + +
26Z PHE* 5.8 1.6 - - + -
27Z GLY* 5.8 9.6 - - - +
30Z SER* 5.4 6.7 - - - +
49Z TYR* 3.9 24.7 - - + -
51Z LEU* 4.2 16.8 - - + -
52Z THR 5.5 0.4 - - - +
53Z LEU* 4.0 28.0 - - + -
128Z ILE* 2.8 43.9 + - + +
129Z ARG* 3.2 3.8 + - - +
131Z VAL* 1.3 74.2 - - + +
133Z ARG* 1.3 65.0 + - + +
135Z ILE* 3.2 9.1 + - + +
136Z THR* 2.7 35.0 + - - +
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Residues in contact with ARG 133 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82P TYR* 4.3 19.1 - - + +
83P GLN* 3.2 54.2 + - - +
84P ARG* 5.6 3.2 - - - +
85P GLN* 4.1 28.5 - - - +
200P PHE* 4.6 15.1 + - - +
202P GLU* 3.7 22.6 + - - -
203P LEU* 5.0 1.6 + - - +
205P ALA* 6.2 0.2 - - - +
51Z LEU* 5.5 2.5 - - + -
126Z ASP 4.6 2.4 + - - -
129Z ARG* 2.9 39.0 + - + +
130Z SER* 3.2 30.4 + - - +
132Z ILE* 1.3 77.9 - - + +
134Z GLN* 1.3 63.2 + - - +
136Z THR* 3.4 7.0 - - - -
137Z ALA* 2.9 19.4 + - - +
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Residues in contact with GLN 134 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83P GLN* 4.4 1.5 + - - -
195P PHE* 3.4 25.1 - - + -
198P ASP* 5.9 0.2 + - - -
130Z SER 2.9 18.9 + - - +
131Z VAL* 3.3 10.0 - - - +
132Z ILE 3.1 0.2 - - - -
133Z ARG* 1.3 76.7 - - - +
135Z ILE* 1.3 63.9 + - - +
137Z ALA* 3.0 9.9 + - - +
138Z THR* 2.9 22.9 + - - +
183Z LEU* 3.3 19.8 - - + +
184Z ARG* 2.7 78.7 + - - +
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Residues in contact with ILE 135 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Z PHE* 5.2 3.1 - - + -
27Z GLY* 5.3 11.0 - - - +
30Z SER* 6.2 2.5 - - - -
31Z ILE* 3.6 39.5 - - + -
34Z GLN* 4.6 2.2 - - - +
100Z TRP* 4.4 8.7 - - + -
102Z PHE* 4.8 13.9 - - + -
131Z VAL* 2.9 40.7 + - + +
132Z ILE* 3.7 7.2 - - - +
134Z GLN* 1.3 73.8 - - - +
136Z THR* 1.3 65.1 + - - +
138Z THR* 2.1 37.0 + - - +
139Z VAL* 3.7 1.2 + - - +
183Z LEU* 3.5 20.2 - - + -
195Z SER* 6.2 0.9 - - - +
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Residues in contact with THR 136 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82P TYR* 3.5 35.2 + - + +
89P LEU* 5.7 0.7 - - + -
90P PRO* 3.6 21.1 - - + -
30Z SER* 5.6 3.1 - - - -
34Z GLN* 3.4 32.4 + - - +
132Z ILE* 2.7 24.6 + - - +
133Z ARG 3.4 8.7 - - - -
135Z ILE* 1.3 79.0 - - - +
137Z ALA* 1.3 64.0 + - - +
138Z THR 3.0 0.3 + - - -
139Z VAL* 3.0 25.9 - - + +
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Residues in contact with ALA 137 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79P HIS* 3.3 23.1 - - + -
83P GLN* 3.3 26.4 - - - +
195P PHE* 5.6 5.8 - - + -
133Z ARG 2.9 8.2 + - - +
134Z GLN* 3.2 11.4 - - - +
136Z THR* 1.3 76.1 - - - +
138Z THR* 1.3 52.1 + - + +
140Z THR* 2.6 45.1 + - - +
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Residues in contact with THR 138 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195P PHE* 3.5 30.3 - - + -
100Z TRP* 3.5 22.9 - - + -
134Z GLN 2.9 19.7 + - - +
135Z ILE* 2.1 35.1 + - - +
137Z ALA* 1.3 75.1 - - - +
139Z VAL* 1.3 61.2 + - - +
140Z THR 3.0 1.3 + - - -
141Z PHE* 3.1 36.9 + - + -
142Z LEU* 3.2 12.4 - - - +
183Z LEU* 4.0 12.1 - - + -
197Z VAL* 5.9 0.2 - - - -
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Residues in contact with VAL 139 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90P PRO* 6.0 4.9 - - + -
93P GLN* 5.8 1.8 - - - +
34Z GLN* 3.8 26.9 - - + +
35Z ARG* 3.3 44.1 + - - +
135Z ILE 3.7 0.4 + - - +
136Z THR* 3.0 24.0 + - + +
137Z ALA 2.8 1.9 + - - +
138Z THR* 1.3 81.7 + - - +
140Z THR* 1.3 67.2 + - + +
141Z PHE 2.9 6.3 + - - -
142Z LEU* 3.6 11.1 + - - +
144Z LEU* 5.5 2.6 - - - +
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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