Contacts of the helix formed by residues 116 - 130 (chain B) in PDB entry 3EQ6
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 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B TRP* 3.7 8.5 - - + +
113B LEU* 4.6 4.3 - - + -
114B PRO* 2.9 30.3 + - + +
115B ARG* 1.3 80.0 - - - +
117B PRO* 1.3 73.6 - - + +
118B GLU* 2.9 21.0 + - + +
119B TRP* 3.0 17.0 + - - +
120B TRP* 3.2 13.4 - - - -
183B VAL* 4.4 15.3 - - + -
195B LYS* 6.2 0.7 - - - +
287B LEU* 3.8 15.5 - - + -
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Residues in contact with PRO 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.2 8.7 - - + +
71B TRP* 3.6 40.1 - - + +
79B LEU* 4.2 8.1 - - + -
81B TRP* 3.3 40.4 - - + -
116B VAL* 1.3 88.2 - - + +
118B GLU* 1.3 67.7 + - - +
120B TRP* 2.9 30.9 + - + +
121B LEU* 3.0 15.6 + - + +
195B LYS* 6.0 0.7 - - - +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TRP* 6.2 0.2 - - - -
113B LEU* 4.1 1.6 - - + -
116B VAL* 2.9 23.5 + - + +
117B PRO* 1.3 83.9 - - - +
119B TRP* 1.3 57.3 + - - +
121B LEU* 4.1 14.8 - - + +
122B VAL* 2.7 35.9 + - - +
183B VAL* 4.0 22.6 - - + +
194B PHE* 3.6 32.1 - - + -
195B LYS* 3.0 38.8 + - + +
198B LEU* 5.1 3.6 - - + +
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Residues in contact with TRP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 3.9 26.7 + - + +
113B LEU* 3.8 23.7 - - + +
114B PRO 4.3 6.7 - - - +
116B VAL* 3.0 13.9 + - - +
118B GLU* 1.3 79.0 - - - +
120B TRP* 1.3 88.5 + + + +
122B VAL* 3.7 1.8 - - - +
123B ILE* 3.0 54.2 + - + +
135B PRO* 4.2 16.6 - - + +
219B TYR* 4.8 1.1 - - - -
263B THR* 3.2 45.5 + - - -
264B GLY* 5.3 0.2 - - - -
268B ASN* 3.1 31.4 - - + -
269B ILE* 4.4 18.6 - - + -
273B LEU* 4.4 14.4 - - + -
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Residues in contact with TRP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.3 13.5 - - + -
86B LEU* 5.4 0.9 - - + -
115B ARG* 4.4 5.6 - - + -
116B VAL 3.2 31.0 - - - -
117B PRO* 2.9 10.3 + - + +
119B TRP* 1.3 97.1 - + + +
121B LEU* 1.3 64.5 + - - +
123B ILE* 3.5 1.2 + - - +
124B LEU* 3.1 30.7 + - - +
263B THR* 4.2 7.9 - - + -
268B ASN* 3.9 18.8 - - - -
272B SER* 3.3 35.2 + - - -
273B LEU* 3.9 22.0 - - + +
277B TRP* 3.7 33.7 - + + -
283B THR* 4.5 4.3 - - + +
285B VAL* 3.4 40.8 - - + -
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 5.5 0.9 - - + -
81B TRP* 4.2 17.9 - - + +
86B LEU* 4.1 24.2 - - + -
89B ASN* 3.1 33.2 - - + +
90B SER* 4.0 21.6 - - - +
93B ALA* 3.2 20.0 - - + +
117B PRO* 3.0 18.3 + - + +
118B GLU* 3.8 17.3 - - + +
119B TRP 3.3 0.2 - - - -
120B TRP* 1.3 78.1 - - + +
122B VAL* 1.3 55.4 + - - +
124B LEU* 3.5 4.6 + - - +
125B GLY 2.8 22.9 + - - -
194B PHE* 5.0 4.7 - - + -
198B LEU* 4.2 15.0 - - + -
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA* 4.5 4.9 - - - -
97B LEU* 3.9 7.4 - - + +
111B VAL* 4.2 31.2 - - + -
113B LEU* 4.4 1.8 - - + -
118B GLU* 2.7 31.0 + - + +
119B TRP* 3.7 4.5 - - - +
121B LEU* 1.3 69.8 - - - +
123B ILE* 1.3 62.2 + - - +
125B GLY* 3.0 2.3 + - - +
126B CYS* 2.8 35.1 + - - -
158B VAL* 4.0 28.9 - - + -
194B PHE* 3.7 30.1 - - + -
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 4.4 17.0 - - + -
119B TRP* 3.0 54.3 + - + +
120B TRP 4.0 3.1 - - - +
122B VAL* 1.3 75.9 - - - +
124B LEU* 1.3 61.8 + - - +
126B CYS* 3.2 6.9 + - - +
127B ILE* 3.0 27.5 + - + +
133B PHE* 3.6 41.5 - - + -
135B PRO* 4.5 2.2 - - + -
269B ILE* 3.5 29.8 - - + -
273B LEU* 4.3 4.5 - - + -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 5.0 7.0 - - + -
47B ALA* 4.9 11.0 - - + -
51B LEU* 3.7 31.6 - - + -
86B LEU* 3.9 13.5 - - + -
90B SER* 3.5 26.9 - - - +
120B TRP 3.1 17.6 + - - +
121B LEU* 3.6 0.7 - - - +
123B ILE* 1.3 78.0 - - - +
125B GLY* 1.3 57.4 + - - +
127B ILE* 3.1 15.6 + - + +
128B ARG* 2.9 36.3 + - - +
273B LEU* 4.6 10.8 - - + -
277B TRP* 3.6 33.4 - - + -
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B SER 3.8 4.2 + - - -
93B ALA* 3.8 4.5 - - - -
94B ALA* 3.6 25.9 - - - +
97B LEU* 3.6 9.4 - - - -
121B LEU 2.8 16.0 + - - -
122B VAL 3.0 5.5 + - - -
124B LEU* 1.3 75.8 - - - +
126B CYS* 1.3 60.6 + - - +
128B ARG 3.3 1.6 + - - -
129B ALA* 3.0 26.0 + - - +
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Residues in contact with CYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 3.6 14.1 - - - +
109B VAL* 4.3 20.2 - - - -
111B VAL* 5.1 0.4 - - - -
122B VAL* 2.8 26.6 + - - -
123B ILE 3.4 7.9 - - - +
125B GLY* 1.3 72.0 - - - +
127B ILE* 1.3 53.6 + - - +
129B ALA 3.1 1.4 + - - -
130B GLY 2.8 15.8 + - - -
131B LEU* 2.8 55.5 + - - +
133B PHE* 3.9 26.7 - - + -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASN* 2.8 48.9 + - - +
46B PHE* 4.3 8.3 - - + +
47B ALA* 4.0 14.4 - - + +
123B ILE* 3.0 30.4 + - + +
124B LEU* 3.1 19.5 + - + +
126B CYS* 1.3 76.5 - - - +
128B ARG* 1.3 62.1 + - - +
130B GLY* 3.6 5.4 + - - -
131B LEU 5.0 0.9 - - - -
133B PHE* 3.7 27.6 - - + -
210B THR* 4.5 0.2 - - - +
216B SER* 4.1 7.6 - - - +
235B TYR* 3.9 18.2 - - + -
269B ILE* 4.9 1.1 - - + -
273B LEU* 5.6 2.0 - - + -
274B MET* 4.5 18.8 - - + -
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 3.8 19.1 - - + +
51B LEU* 3.7 17.0 - - - +
52B ASP* 2.8 43.4 + - - -
87B SER* 3.4 8.9 + - - -
90B SER* 3.3 42.7 + - - -
91B GLN* 3.7 29.4 - - - +
94B ALA* 3.6 14.6 - - + -
124B LEU* 2.9 17.3 + - - +
126B CYS 3.2 0.2 - - - -
127B ILE* 1.3 79.0 - - - +
129B ALA* 1.3 56.6 + - - +
130B GLY 3.2 0.6 + - - -
205B HIS* 3.5 14.2 + - - +
207B CYS* 4.0 18.4 - - - +
208B VAL* 3.0 33.6 + - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ALA* 4.3 10.3 - - + +
97B LEU* 5.0 0.2 - - + -
98B SER* 4.3 22.2 - - - -
105B ARG* 4.1 8.3 + - - +
125B GLY 3.0 16.5 + - - +
128B ARG* 1.3 77.4 - - - +
130B GLY* 1.3 63.4 + - - +
131B LEU* 3.3 30.3 - - + +
205B HIS* 4.1 7.6 - - - +
208B VAL* 3.8 12.8 - - - +
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 3.5 9.5 - - - +
106B GLY* 2.9 26.5 + - - -
126B CYS 2.8 3.8 + - - -
127B ILE 3.6 0.8 + - - -
128B ARG 3.2 5.5 + - - -
129B ALA* 1.3 77.8 - - - +
131B LEU* 1.3 61.2 + - - +
132B ILE* 4.2 1.2 + - - +
208B VAL* 4.6 3.6 - - - -
210B THR* 4.2 13.5 - - - -
214B GLU* 5.0 1.8 - - - +
215B ALA 5.4 1.0 - - - +
235B TYR* 3.1 22.6 + - - -
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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
------------------------------------------------------------
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