Contacts of the strand formed by residues 17 - 24 (chain C) in PDB entry 3SHD
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 LYS 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C HIS* 3.2 9.9 + - - -
14C ALA 3.0 29.8 + - - +
15C GLU 2.7 12.9 + - - +
16C GLY* 1.3 81.0 - - - +
18C PHE* 1.3 64.2 + - - +
91C ILE* 4.0 9.0 - - + -
106C TRP* 3.5 39.3 - - + +
107C VAL* 3.3 18.4 - - - +
108C SER* 4.1 5.1 - - - +
111C GLU* 4.3 10.6 + - - -
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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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11C VAL* 3.7 24.7 - - + -
12C VAL 3.2 8.5 - - - +
13C HIS* 3.4 30.5 - + + -
16C GLY 4.5 3.8 - - - -
17C LYS* 1.3 76.4 - - - +
19C LEU* 1.3 64.1 + - - +
20C VAL* 3.5 2.3 + - - +
105C ARG 3.5 0.5 - - - +
106C TRP* 3.5 5.9 - - - -
107C VAL* 2.6 34.4 + - - +
108C SER 4.0 0.2 - - - -
109C ALA* 3.5 46.2 - - + -
112C ILE* 3.8 17.9 - - + -
127C ILE* 4.6 11.2 - - + -
130C TYR* 3.7 34.3 - + - -
131C GLN* 4.8 7.4 - - + -
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Residues in contact with LEU 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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12C VAL* 2.8 32.0 + - + +
18C PHE* 1.3 72.8 - - - +
20C VAL* 1.3 69.5 + - - +
33C GLN* 4.4 5.0 - - - +
34C PRO* 3.4 25.7 - - + +
52C LEU* 4.3 6.3 - - + -
56C THR* 3.8 22.9 - - + -
58C ILE* 3.7 28.9 - - + -
94C THR* 4.2 1.8 - - + -
104C CYS* 3.7 22.2 - - + -
105C ARG 3.6 11.2 - - - +
106C TRP* 3.7 32.2 - - + +
112C ILE* 5.6 0.2 - - - +
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Residues in contact with VAL 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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18C PHE 4.5 3.4 - - - +
19C LEU* 1.3 77.3 - - - +
21C VAL* 1.3 63.0 + - - +
31C TRP* 3.7 47.8 - - + -
32C ASN 3.3 23.3 - - - +
33C GLN* 4.5 6.5 - - - +
34C PRO* 4.6 0.2 - - - -
104C CYS* 3.3 9.2 - - - +
105C ARG* 3.0 45.6 + - + +
107C VAL* 4.9 3.6 - - + -
112C ILE* 4.2 25.1 - - + -
123C VAL* 5.2 2.7 - - + -
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Residues in contact with VAL 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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20C VAL* 1.3 79.7 - - - +
22C GLU* 1.3 61.0 + - - +
23C GLU* 4.3 11.7 - - - +
30C LEU 3.4 1.6 - - - +
31C TRP* 3.4 5.3 - - - -
32C ASN* 2.9 42.0 + - + +
33C GLN 4.0 8.7 - - - +
34C PRO* 3.7 15.0 - - + -
55C GLU* 4.0 24.9 - - + +
56C THR* 3.5 32.3 - - + -
101C ILE* 4.4 12.3 - - + -
103C CYS 3.8 6.3 - - - +
104C CYS* 4.3 2.0 - - - -
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Residues in contact with GLU 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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20C VAL* 4.2 1.2 + - - +
21C VAL* 1.3 69.7 - - - +
23C GLU* 1.3 62.9 + - - +
29C ALA* 3.9 24.5 - - + +
30C LEU 3.2 3.1 - - - -
31C TRP* 3.0 33.7 + - + +
101C ILE* 3.9 2.9 - - - +
102C ASP* 2.9 35.0 + - + +
103C CYS* 3.0 29.1 + - - +
104C CYS* 4.6 0.2 - - - +
105C ARG* 3.1 39.2 + - + -
117C ASN* 5.5 0.2 - - - -
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Residues in contact with GLU 23 (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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21C VAL* 4.3 10.2 - - - +
22C GLU* 1.3 76.1 - - - +
24C THR* 1.3 69.0 + - - +
25C ILE* 3.3 10.4 + - + +
29C ALA* 4.1 0.7 - - - -
30C LEU* 2.6 41.5 + - + +
32C ASN* 4.4 5.8 - - - +
100C ASP* 3.5 24.4 - - + +
101C ILE* 3.6 18.8 - - + +
102C ASP* 3.8 2.5 - - - -
119C ARG* 3.5 24.7 + - + +
157C SO4 3.0 36.3 + - - -
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Residues in contact with THR 24 (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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23C GLU* 1.3 74.8 - - - +
25C ILE* 1.3 68.9 + - - +
26C ASN* 4.3 9.0 - - - +
27C GLY 4.5 11.6 + - - +
28C LYS 3.6 8.2 - - - +
29C ALA* 4.0 12.9 + - - +
100C ASP 4.7 3.0 + - - +
102C ASP* 2.8 30.6 + - - -
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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
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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