Contacts of the helix formed by residues 108 - 126 (chain P) in PDB entry 3SDI
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 108 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P TYR* 3.6 24.5 - - + +
106P ASP 3.5 6.9 - - - +
107P ILE* 1.3 89.4 - - + +
109P VAL* 1.3 65.7 + - - +
110P GLU* 4.6 3.1 - - + +
111P ILE* 3.0 35.9 + - + +
112P LEU* 3.3 9.5 + - - +
142P ASP* 3.6 21.1 - - + +
144P ARG* 5.9 8.3 - - + -
66X TYR* 4.6 1.6 - - - +
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Residues in contact with VAL 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P ILE* 4.0 25.6 - - + -
107P ILE 3.4 1.8 + - - +
108P PRO* 1.3 68.6 - - - +
110P GLU* 1.3 65.4 + - - +
111P ILE 3.2 0.2 + - - -
112P LEU* 3.2 3.8 + - - +
113P VAL* 3.0 26.7 + - + +
138P TYR* 5.0 2.7 - - + -
140P GLY* 3.8 18.2 - - - +
141P TYR 3.8 31.9 - - - +
142P ASP* 3.2 15.1 + - - +
147P GLN* 3.6 16.6 - - + +
149P TYR* 3.7 25.1 - - + -
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Residues in contact with GLU 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108P PRO* 3.3 4.2 - - + +
109P VAL* 1.3 76.6 - - - +
111P ILE* 1.3 56.4 + - + +
113P VAL* 3.0 5.3 + - - +
114P ARG* 2.7 60.3 + - - +
142P ASP* 4.7 0.2 + - - -
144P TYR* 4.3 24.0 + - - +
147P GLN* 3.9 5.4 + - - +
149P TYR* 3.8 22.4 + - + +
157P TYR* 3.3 29.0 + - + +
62Q ILE 4.3 14.9 - - - +
64Q PRO* 5.4 5.2 - - - +
70X GLU* 6.0 1.6 - - - +
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Residues in contact with ILE 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95P HIS* 4.1 8.7 - - + +
99P TYR* 4.1 10.1 - - + -
107P ILE* 3.6 19.1 - - + -
108P PRO* 3.0 33.5 + - + +
110P GLU* 1.3 78.2 - - + +
112P LEU* 1.3 63.3 + - - +
114P ARG* 3.3 15.8 + - - +
115P ARG* 3.0 22.3 + - - +
66X TYR* 3.4 23.1 - - + +
70X GLU* 3.1 42.4 - - + +
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Residues in contact with LEU 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70P LEU* 3.6 37.7 - - + -
71P ASN* 5.4 0.2 - - + -
74P ILE* 4.1 17.0 - - + -
92P ALA* 4.1 21.5 - - + +
95P HIS* 4.3 7.2 - - + -
96P ALA* 4.2 8.1 - - + -
107P ILE* 3.7 36.0 - - + +
108P PRO 3.3 3.3 + - - +
109P VAL 3.2 7.0 + - - +
111P ILE* 1.3 78.3 - - - +
113P VAL* 1.3 69.2 + - + +
115P ARG* 3.2 5.5 + - - +
116P LEU* 3.1 26.6 + - + +
138P TYR* 4.3 13.5 - - + -
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Residues in contact with VAL 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P ILE* 6.1 0.2 - - + -
109P VAL* 3.0 17.9 + - + +
110P GLU* 3.0 10.2 + - - +
112P LEU* 1.3 76.6 - - + +
114P ARG* 1.3 66.3 + - - +
116P LEU* 3.3 3.2 + - - +
117P SER* 3.0 25.7 + - - +
138P TYR* 3.5 55.8 + - + -
149P TYR* 4.0 17.5 - - + -
157P TYR* 3.6 36.8 - - + -
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Residues in contact with ARG 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110P GLU* 2.7 45.9 + - - +
111P ILE* 3.7 18.2 + - - +
113P VAL* 1.3 72.5 - - - +
115P ARG* 1.3 63.6 + - - +
117P SER* 3.3 2.4 + - - -
118P ASP* 2.9 38.3 + - - +
157P TYR* 3.7 23.3 + - - +
86Q ARG* 3.8 30.6 - - - +
90Q GLU* 6.0 1.3 - - - -
93Q ARG* 6.0 1.1 - - - +
69X ARG* 3.9 26.5 + - - +
70X GLU* 2.6 36.9 + - - -
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Residues in contact with ARG 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95P HIS* 3.8 44.9 + - + +
111P ILE 3.0 12.4 + - - +
112P LEU 3.2 9.8 + - - +
114P ARG* 1.3 76.4 - - - +
116P LEU* 1.3 61.6 + - + +
118P ASP* 3.2 26.9 + - - +
119P ILE* 3.1 49.6 + - + +
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Residues in contact with LEU 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70P LEU* 4.9 1.8 - - + -
76P VAL* 5.7 0.4 - - + -
88P LEU* 3.5 46.9 - - + +
89P ILE* 5.6 0.4 - - - -
91P THR* 4.3 9.6 - - - +
92P ALA* 3.7 28.0 - - + -
112P LEU* 3.1 14.5 + - + +
113P VAL 3.3 4.5 + - - +
115P ARG* 1.3 76.7 - - + +
117P SER* 1.3 63.3 + - - +
119P ILE* 3.2 11.0 + - + +
120P LYS* 3.1 28.0 + - - +
136P PHE* 4.2 12.1 - - + -
138P TYR* 3.3 39.5 - - + +
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Residues in contact with SER 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P VAL* 3.0 17.5 + - - +
114P ARG 3.6 3.1 - - - -
116P LEU* 1.3 74.7 - - - +
118P ASP* 1.3 51.7 + - - +
120P LYS* 3.2 8.5 + - - -
121P GLN* 2.8 31.5 + - - +
138P TYR* 5.1 0.2 + - - -
151P SER* 3.7 11.0 - - - -
155P GLY* 3.2 33.7 - - - -
157P TYR* 3.4 29.0 - - - +
86Q ARG* 3.3 9.6 - - - -
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Residues in contact with ASP 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P ARG* 2.9 31.0 + - - +
115P ARG* 3.3 27.3 + - - +
117P SER* 1.3 73.0 - - - +
119P ILE* 1.3 64.6 + - - +
121P GLN* 3.3 8.2 + - - +
122P GLY* 3.0 19.4 + - - -
86Q ARG* 2.8 33.7 + - - +
87Q ILE* 3.8 16.6 - - + +
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Residues in contact with ILE 119 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P LEU* 3.8 20.4 - - + -
91P THR* 3.5 28.5 - - + +
115P ARG* 3.1 43.2 + - + +
116P LEU* 3.2 17.2 + - + +
118P ASP* 1.3 74.8 - - - +
120P LYS* 1.3 63.7 + - - +
122P GLY* 3.2 10.7 + - - -
123P TYR* 3.3 29.9 - - + -
132P PHE* 4.4 2.0 - - + -
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Residues in contact with LYS 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P LEU* 3.9 30.3 - - + -
116P LEU* 3.1 14.4 + - - +
117P SER* 3.4 10.8 - - - +
119P ILE* 1.3 76.6 - - - +
121P GLN* 1.3 66.1 + - - +
123P TYR* 3.0 20.1 + - - +
124P THR* 3.3 9.2 + - - -
131P PRO* 5.8 0.3 - - - +
132P PHE* 4.7 12.1 - - + -
134P VAL* 3.7 16.8 + - - -
136P PHE* 3.4 19.9 - - - -
138P TYR* 5.0 1.1 - - - -
151P SER* 2.7 44.2 + - - +
152P ASN 3.6 15.0 - - - +
153P PRO* 4.1 14.2 - - + +
155P GLY* 3.9 9.0 - - - +
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Residues in contact with GLN 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117P SER 2.8 19.8 + - - +
118P ASP* 3.6 9.6 + - - +
120P LYS* 1.3 73.0 - - - +
122P GLY* 1.3 65.9 + - - +
124P THR* 2.8 30.6 - - - -
125P GLN* 2.8 34.3 + - - +
126P HIS* 5.6 1.2 + - - -
154P SER 4.3 1.6 - - - +
155P GLY* 3.8 4.6 - - - -
83Q ALA* 3.5 37.2 - - + +
84Q ASP* 3.0 19.6 - - - +
86Q ARG* 4.4 2.2 - - - +
87Q ILE* 3.4 26.9 - - + +
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Residues in contact with GLY 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P ASP 3.0 13.6 + - - -
119P ILE 3.2 5.8 + - - -
120P LYS 3.0 1.2 + - - -
121P GLN* 1.3 83.1 - - - +
123P TYR* 1.3 58.2 + - - +
125P GLN* 2.9 17.0 + - - -
126P HIS* 2.9 39.9 + - - +
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Residues in contact with TYR 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125O GLN* 3.5 19.8 + - - -
13P THR* 4.2 8.8 - - - -
119P ILE* 3.3 25.1 - - + -
120P LYS 3.0 8.0 + - - +
122P GLY* 1.3 76.3 - - - +
124P THR* 1.3 61.5 + - - +
125P GLN 3.6 0.2 + - - -
126P HIS 4.0 11.8 - - - +
129P LEU* 3.8 45.4 - - + +
130P ARG 3.5 17.5 - - - +
131P PRO* 4.0 23.3 - - + +
132P PHE* 3.4 34.0 - + + -
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Residues in contact with THR 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P THR* 3.6 16.5 - - - +
21P LEU* 3.7 17.8 - - + +
24P VAL* 3.8 16.0 - - + +
120P LYS 3.3 3.5 + - - -
121P GLN* 2.8 20.4 + - + +
123P TYR* 1.3 79.8 - - - +
125P GLN* 1.3 54.4 + - - +
131P PRO* 5.2 2.9 - - - +
153P PRO 3.5 20.5 + - - -
154P SER 4.0 10.9 + - - +
84Q ASP* 4.4 3.1 - - - +
130Q ARG* 2.9 50.2 + - - +
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Residues in contact with GLN 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P THR* 4.8 3.9 - - - -
121P GLN* 2.8 36.6 + - - +
122P GLY 2.9 4.7 + - - +
124P THR* 1.3 78.4 - - - +
126P HIS* 1.3 68.9 + - + +
84Q ASP* 4.1 0.2 - - - +
87Q ILE* 4.8 4.0 - - - +
123Q TYR* 3.7 16.9 + - + -
128Q GLY 3.9 0.2 - - - +
129Q VAL* 3.4 1.7 - - - -
130Q ARG* 3.1 62.3 + - + +
131Q PRO 3.8 3.8 - - - +
132Q PHE* 3.3 44.7 - - - -
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Residues in contact with HIS 126 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P THR* 4.8 3.1 - - - -
121P GLN* 5.6 1.2 + - - -
122P GLY* 2.9 36.7 + - - +
123P TYR* 4.0 14.4 + - - +
124P THR 3.8 0.6 - - - -
125P GLN* 1.3 92.7 - - + +
127P GLY* 1.3 63.2 + - - +
128P GLY 3.4 5.9 + - - -
129P LEU* 4.6 2.6 + - - +
123Q TYR* 5.0 12.0 + + - -
128Q GLY 3.2 14.1 - - - +
129Q VAL* 3.7 17.5 - - + -
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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
------------------------------------------------------------
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