Contacts of the helix formed by residues 3 - 15 (chain B) in PDB entry 1SFX
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 ASN 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A VAL* 4.0 6.9 - - - +
25A TYR* 3.8 10.8 - - + -
26A SER* 2.7 36.1 + - - +
29A LEU* 4.5 7.2 - - + -
2B SER* 1.3 79.6 + - - +
4B PRO* 1.3 74.5 - - + +
5B LEU* 3.0 13.3 + - - +
6B GLY* 3.0 28.7 + - - +
7B GLU* 3.1 23.4 + - - +
104B PHE* 3.5 5.6 - - - -
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Residues in contact with PRO 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 3.4 30.5 - - + +
29A LEU* 4.2 1.6 - - + -
82A PRO* 3.7 24.9 - - + -
85A VAL* 4.3 10.1 - - + -
86A LEU* 4.2 17.3 - - + -
3B ASN* 1.3 89.7 - - + +
5B LEU* 1.3 58.3 + - - +
7B GLU* 3.4 3.9 + - + +
8B LEU* 2.9 33.2 + - - +
100B ILE* 4.6 2.0 - - + +
104B PHE* 3.3 29.8 - - + -
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Residues in contact with LEU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.5 41.6 - - + -
21A ASP 3.9 14.1 - - - +
22A VAL* 4.2 11.4 - - + -
25A TYR* 3.5 39.9 - - + -
57A LEU* 4.5 10.5 - - + -
62A PHE* 4.1 6.3 - - + -
85A VAL* 3.5 26.7 - - + -
3B ASN* 3.0 9.5 + - - +
4B PRO* 1.3 73.4 - - - +
6B GLY* 1.3 61.6 - - - +
8B LEU* 3.2 6.6 + - + +
9B VAL* 2.9 34.2 + - - +
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Residues in contact with GLY 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.9 15.3 - - - +
3B ASN* 3.0 20.9 + - - -
5B LEU* 1.3 74.8 - - - +
7B GLU* 1.3 63.5 + - - +
9B VAL* 3.4 8.8 + - - +
10B LYS* 3.2 29.8 + - - +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER* 4.3 10.9 + - - +
3B ASN 3.1 20.1 + - - +
4B PRO 3.8 4.3 - - - +
6B GLY* 1.3 73.5 - - - +
8B LEU* 1.3 60.0 + - - +
10B LYS* 2.9 38.2 + - - +
11B ALA* 3.0 28.4 + - - +
99B ARG* 4.6 9.2 + - - -
100B ILE* 3.7 25.8 - - + +
103B MSE 3.6 39.3 - - + +
104B PHE* 4.6 1.6 - - + -
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Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.0 20.6 - - + -
85A VAL* 4.5 4.0 - - + -
86A LEU* 3.9 28.0 - - + -
89A PHE* 3.9 48.9 - - + -
4B PRO 2.9 22.0 + - - +
5B LEU* 3.6 13.7 - - + +
7B GLU* 1.3 73.5 - - - +
9B VAL* 1.3 65.6 + - - +
11B ALA* 3.9 3.3 - - + +
12B LEU* 2.8 34.5 + - + +
97B ILE* 4.4 9.2 - - + -
100B ILE* 4.0 13.9 - - + -
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.0 25.1 - - + +
22A VAL* 4.0 22.0 - - + -
5B LEU 2.9 18.6 + - - +
6B GLY* 3.6 9.4 - - - +
7B GLU 3.3 0.2 - - - -
8B LEU* 1.3 76.2 - - - +
10B LYS* 1.3 66.4 + - + +
12B LEU* 3.4 7.7 + - - +
13B GLU* 3.0 23.2 + - + +
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Residues in contact with LYS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLY 3.2 14.0 + - - +
7B GLU* 2.9 40.9 + - - +
8B LEU 3.2 0.2 - - - -
9B VAL* 1.3 80.7 - - + +
11B ALA* 1.3 61.3 + - - +
13B GLU* 3.3 8.7 + - - +
14B LYS* 3.1 26.7 + - + +
99B ARG* 6.2 0.9 - - - +
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU 3.0 17.0 + - - +
8B LEU* 3.9 5.8 - - + +
10B LYS* 1.3 76.6 - - - +
12B LEU* 1.3 59.3 + - + +
14B LYS* 3.3 7.9 + - - +
15B LEU* 3.0 35.2 + - + +
96B GLU* 3.6 32.7 - - + +
99B ARG* 4.4 4.4 - - - +
100B ILE* 4.0 16.6 - - + -
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.6 34.8 - - + +
15A LEU* 4.6 5.8 - - + +
16A SER* 5.1 6.3 - - - -
17A PHE* 4.3 15.7 - - + -
89A PHE* 3.8 37.5 - - + -
8B LEU* 2.8 30.5 + - + +
9B VAL* 3.8 5.2 - - - +
11B ALA* 1.3 75.4 - - + +
13B GLU* 1.3 60.0 + - - +
15B LEU* 3.6 4.8 - - + +
16B SER* 3.0 26.9 + - - -
93B ILE* 3.9 15.9 - - + -
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.0 16.0 + - + +
10B LYS* 3.4 11.7 - - - +
11B ALA 3.3 0.2 - - - -
12B LEU* 1.3 77.0 - - - +
14B LYS* 1.3 63.7 + - + +
16B SER* 2.5 34.7 + - - -
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS* 3.1 15.3 + - + +
11B ALA* 3.3 10.1 + - - +
13B GLU* 1.3 81.9 - - + +
15B LEU* 1.3 65.3 + - + +
16B SER 3.3 4.4 + - - +
60B ARG* 4.4 6.1 + - - -
96B GLU* 4.9 11.7 - - - +
99B ARG* 6.2 0.7 - - - +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.9 4.8 - - + +
11B ALA* 3.0 23.6 + - + +
12B LEU* 3.4 8.3 + - + +
13B GLU 3.2 0.2 - - - -
14B LYS* 1.3 80.3 - - + +
16B SER* 1.3 64.1 + - - +
17B PHE* 3.9 8.5 - - - -
60B ARG* 2.9 36.5 + - - +
89B PHE* 3.9 13.2 - - + -
92B SER* 4.3 22.4 - - - -
93B ILE* 3.8 43.5 - - + -
96B GLU* 4.2 21.8 - - + -
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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