Contacts of the helix formed by residues 3 - 15 (chain X) in PDB entry 3F6E
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 3 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X ALA* 1.3 74.9 - - - +
4X VAL* 1.3 59.3 + - - +
5X HIS* 3.5 7.4 + - - +
6X GLY* 3.0 20.6 + - - +
7X THR* 2.9 31.2 + - - -
163X TRP 3.7 11.9 - - - -
164X ASP* 4.4 10.1 - - - -
165X LYS 3.3 10.1 - - - -
166X ASP* 4.5 2.0 - - - +
167X ALA* 3.8 2.2 - - - -
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Residues in contact with VAL 4 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3X SER* 1.3 68.8 - - - +
5X HIS* 1.3 63.4 + - - +
7X THR* 3.3 2.0 + - - -
8X THR* 2.8 33.3 + - - +
132X ALA 3.4 23.1 - - - +
133X ALA* 4.4 1.3 - - - -
135X VAL* 3.7 34.5 - - + -
136X PRO* 4.1 5.4 - - + -
162X ASP 3.3 24.9 - - - +
163X TRP* 3.4 11.2 + - + +
165X LYS* 2.8 20.7 + - + +
166X ASP 4.0 12.1 - - - +
167X ALA* 3.9 12.1 - - + +
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Residues in contact with HIS 5 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3X SER* 3.6 6.5 + - - +
4X VAL* 1.3 76.5 - - - +
6X GLY* 1.3 67.4 + - - +
8X THR* 3.8 0.7 - - - -
9X TYR* 3.1 48.6 + + - -
30X PRO 3.3 24.0 - - - -
31X PHE* 3.2 17.6 + - - -
33X LYS* 2.8 36.1 + - + +
34X ASP* 3.8 19.7 - - + -
36X PRO* 5.2 0.7 - - + -
163X TRP* 2.9 33.3 + + + +
164X ASP* 5.0 2.7 - - - +
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Residues in contact with GLY 6 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X ALA* 5.5 2.7 - - - -
3X SER* 3.0 19.0 + - - -
5X HIS* 1.3 81.7 + - - +
7X THR* 1.3 57.4 + - - +
9X TYR* 3.6 4.4 + - - +
10X GLU* 3.1 28.3 + - - +
13X ARG* 4.9 1.6 + - - -
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Residues in contact with THR 7 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X ALA* 3.5 13.4 - - - +
3X SER 2.9 17.4 + - - -
4X VAL 3.8 3.4 - - - -
6X GLY* 1.3 73.0 - - - +
8X THR* 1.3 61.4 + - - +
10X GLU* 3.4 5.0 + - - -
11X LEU* 2.9 28.1 + - - +
136X PRO* 3.7 22.0 - - + -
167X ALA* 3.2 17.7 - - + +
171X SER* 3.8 23.8 - - - -
175X PHE* 3.5 19.7 - - + -
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Residues in contact with THR 8 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X VAL* 2.8 23.1 + - - +
5X HIS 3.8 2.5 - - - -
6X GLY 3.2 0.2 - - - -
7X THR* 1.3 76.6 - - - +
9X TYR* 1.3 61.9 + - - +
11X LEU* 3.2 7.1 + - - +
12X LEU* 2.9 35.7 + - + +
31X PHE* 4.7 3.8 - - + -
135X VAL* 4.0 3.3 - - + +
136X PRO* 3.8 17.4 - - - +
139X MET* 3.8 39.7 - - + -
163X TRP* 3.6 23.3 - - + -
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Residues in contact with TYR 9 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5X HIS* 3.1 52.7 + + - +
6X GLY* 4.1 4.0 - - - +
8X THR* 1.3 76.5 - - - +
10X GLU* 1.3 57.2 + - - +
12X LEU* 3.3 9.0 + - + +
13X ARG* 3.0 38.7 + - - +
20X VAL* 4.9 1.3 - - + -
31X PHE* 2.8 65.4 + + - -
35X PHE* 3.5 23.8 - + - -
36X PRO* 3.5 39.3 - - + -
39X PHE* 3.8 25.8 - + - -
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Residues in contact with GLU 10 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X GLY 3.1 19.1 + - - +
7X THR* 3.6 5.4 - - - +
9X TYR* 1.3 74.4 - - - +
11X LEU* 1.3 65.0 + - - +
13X ARG* 2.8 40.3 + - - +
14X ARG* 2.9 63.8 + - - +
175X PHE* 3.7 30.1 - - + -
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Residues in contact with LEU 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X THR 2.9 14.6 + - - +
8X THR* 3.5 8.5 - - - +
10X GLU* 1.3 74.4 - - - +
12X LEU* 1.3 63.3 + - - +
14X ARG* 3.3 2.5 + - - -
15X GLN* 3.0 37.2 + - + +
136X PRO* 3.3 31.9 - - + +
139X MET* 3.9 15.0 - - + -
140X SER* 3.5 22.9 - - - +
143X ILE* 3.9 8.7 - - + -
144X HIS* 6.0 0.7 - - - +
174X LEU* 3.5 40.6 - - + +
175X PHE* 3.7 15.3 - - + -
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Residues in contact with LEU 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X THR* 2.9 29.9 + - + +
9X TYR* 3.6 28.5 - - + +
10X GLU 3.3 0.2 - - - -
11X LEU* 1.3 77.0 - - - +
13X ARG* 1.3 61.1 + - - +
15X GLN* 3.1 6.4 + - - +
16X GLY 3.1 5.7 + - - -
17X ILE* 2.9 51.4 + - + +
20X VAL* 5.9 0.2 - - + -
31X PHE* 4.7 2.0 - - + -
39X PHE* 3.8 16.6 - - + -
66X PHE* 3.9 39.3 - - + -
139X MET* 4.2 8.3 - - + -
143X ILE* 4.1 13.5 - - + -
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Residues in contact with ARG 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X GLY 4.9 1.2 + - - -
9X TYR* 3.0 17.4 + - - +
10X GLU* 2.8 63.3 + - - +
12X LEU* 1.3 75.5 - - - +
14X ARG* 1.3 62.8 + - + +
16X GLY* 3.0 17.8 + - - -
17X ILE 3.5 10.5 + - - +
18X ASP* 6.2 0.7 - - + -
36X PRO* 3.3 25.1 - - - +
38X ASP* 2.9 42.5 + - - +
39X PHE* 3.7 14.0 - - + -
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Residues in contact with ARG 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10X GLU* 2.9 65.4 + - - +
11X LEU 3.8 2.7 - - - +
13X ARG* 1.3 78.0 - - + +
15X GLN* 1.3 63.1 + - - +
16X GLY 3.3 0.4 + - - -
172X HIS 5.2 1.0 + - - -
175X PHE* 3.3 52.7 - - + +
176X ASP* 2.8 44.0 + - - +
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Residues in contact with GLN 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X LEU* 3.0 32.7 + - + +
12X LEU 3.8 2.9 - - - +
14X ARG* 1.3 80.9 + - - +
16X GLY* 1.3 58.5 + - - +
17X ILE* 3.5 9.3 + - + +
64X PRO* 5.7 3.8 - - - +
143X ILE* 4.0 30.4 - - + +
144X HIS* 3.4 26.5 - - - +
174X LEU 3.9 4.0 + - - -
175X PHE 2.9 22.4 + - - -
176X ASP* 4.1 1.4 - - - +
177X ARG 3.1 27.4 + - - +
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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