Contacts of the helix formed by residues 14 - 22 (chain C) in PDB entry 5SWW
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 ASP 14 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU 4.2 0.8 + - - -
13C MET* 1.3 78.1 - - - +
15C PRO* 1.3 78.2 - - - +
16C HIS* 3.4 28.2 + - - +
17C ILE* 3.2 23.0 + - + +
18C PHE* 3.2 17.3 + - - +
166C VAL* 4.8 0.2 - - - -
167C ASP* 5.8 0.2 - - - -
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Residues in contact with PRO 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C MET 3.5 3.8 - - - +
14C ASP* 1.3 96.3 - - - +
16C HIS* 1.3 57.2 + - - +
18C PHE* 3.2 2.9 + - + +
19C THR* 2.8 34.2 + - + +
162C TRP* 4.2 17.0 - - + -
166C VAL* 4.0 18.8 - - + -
167C ASP* 3.8 24.7 - - + +
168C HIS* 5.5 0.2 - - - -
169C GLN* 6.2 0.9 - - - +
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Residues in contact with HIS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASP* 3.3 13.9 + - - +
15C PRO* 1.3 78.6 - - - +
17C ILE* 1.3 67.3 + - + +
19C THR* 3.7 7.4 - - - -
20C SER* 2.7 55.8 + - - -
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Residues in contact with ILE 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C MET* 4.5 10.8 - - + -
14C ASP* 3.2 29.0 + - + +
16C HIS* 1.3 91.5 - - + +
18C PHE* 1.3 57.9 + - - +
20C SER* 4.3 0.9 - - - -
21C ASN* 2.8 43.1 + - - +
22C PHE* 4.8 0.2 - - - -
30C LYS* 4.7 11.9 - - - +
32C TYR* 3.4 47.1 - - + +
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Residues in contact with PHE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C MET* 3.5 27.3 - - + -
14C ASP 3.2 8.3 + - - +
15C PRO 3.6 5.6 - - - +
17C ILE* 1.3 76.9 - - - +
19C THR* 1.3 63.8 + - + +
20C SER 3.1 0.2 + - - -
22C PHE* 2.8 75.8 + + + +
158C PHE* 3.7 31.0 - + - -
161C CYS* 3.6 23.6 - - + -
162C TRP* 3.8 31.9 - + + -
166C VAL* 3.6 11.7 - - + -
173C PHE* 4.0 16.2 - + - -
176C TRP* 4.4 7.6 - + - -
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Residues in contact with THR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO* 2.8 23.1 + - + +
16C HIS* 3.7 9.0 + - - -
18C PHE* 1.3 87.8 - - + +
20C SER* 1.3 60.9 + - - +
22C PHE 4.6 0.7 - - - -
23C ASN* 3.7 22.5 + - - +
26C ILE* 5.7 0.5 - - - +
28C ARG* 5.7 0.2 + - - -
162C TRP* 4.1 15.5 - - + -
173C PHE* 5.5 2.5 - - + -
174C GLN 6.1 0.7 - - - +
176C TRP* 4.7 20.1 - - + -
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Residues in contact with SER 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C HIS* 2.7 42.1 + - - -
17C ILE* 3.8 3.1 - - - -
19C THR* 1.3 79.4 - - - +
21C ASN* 1.3 68.8 + - - +
23C ASN* 4.2 6.6 - - - +
26C ILE 4.6 0.9 - - - +
28C ARG* 3.0 46.6 + - - +
30C LYS* 5.9 0.7 - - - -
-2G A 5.1 4.2 + - - -
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Residues in contact with ASN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ILE* 2.8 47.6 + - - +
20C SER* 1.3 81.8 + - - +
22C PHE* 1.3 60.1 + - + +
23C ASN 3.2 4.7 - - - -
28C ARG* 3.9 13.7 - - - +
30C LYS* 3.4 39.9 - - - +
32C TYR* 3.4 23.9 - - + -
97C SER* 3.0 15.5 + - - +
128C ARG* 2.3 33.8 + - - +
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Residues in contact with PHE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C MET* 4.4 7.2 - - + -
17C ILE 5.4 0.2 - - - -
18C PHE* 2.8 59.4 + + + +
21C ASN* 1.3 74.2 - - + +
23C ASN* 1.3 63.1 + - - +
24C ASN 3.2 3.8 + - - -
32C TYR* 3.9 30.3 - + + -
34C CYS* 3.7 20.6 - - - -
95C PHE* 3.2 37.7 - - + -
96C ILE 4.1 7.4 - - - -
97C SER* 4.1 4.0 - - - -
127C ALA* 3.9 11.4 - - + +
128C ARG* 4.2 1.1 - - - +
153C MET* 4.1 21.5 - - + -
158C PHE* 3.3 24.2 - - + -
161C CYS* 5.3 0.7 - - - -
176C TRP* 3.3 6.1 - - + -
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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