Contacts of the strand formed by residues 17 - 24 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H VAL 3.7 0.2 - - - +
13H HIS* 3.4 6.5 + - - -
14H ALA 2.9 31.0 + - - +
15H GLU 3.4 12.6 - - - +
16H GLY* 1.3 87.5 - - - +
18H PHE* 1.3 67.2 + - - +
91H ILE* 4.4 13.7 - - + -
106H TRP* 3.9 25.0 + - + +
107H VAL 3.1 17.5 - - - +
108H SER* 4.1 23.7 - - - +
111H GLU* 4.6 5.9 + - - -
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Residues in contact with PHE 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H VAL* 3.7 26.0 - - + -
12H VAL 3.3 14.8 - - - +
13H HIS* 3.1 37.9 - + + -
16H GLY 5.1 2.2 - - - -
17H LYS* 1.3 77.8 - - - +
19H LEU* 1.3 62.3 + - - +
20H VAL* 3.5 2.1 + - + +
105H ARG 3.3 4.9 - - - +
106H TRP* 3.4 3.3 - - - -
107H VAL* 2.6 47.7 + - - +
108H SER 4.3 0.4 - - - -
109H ALA* 3.7 36.3 - - + -
112H ILE* 3.9 14.4 - - + -
127H ILE* 4.3 20.6 - - + -
130H TYR* 3.6 23.8 - + - -
131H GLN* 5.5 1.8 - - + -
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Residues in contact with LEU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H CYS 4.8 1.7 - - - +
12H VAL* 3.2 25.9 + - + +
18H PHE* 1.3 72.0 - - - +
20H VAL* 1.3 68.4 + - - +
33H GLN* 4.4 3.1 - - - +
34H PRO* 3.3 31.3 - - + +
52H LEU* 4.5 2.9 - - + -
56H THR* 3.7 15.5 - - + +
58H ILE* 3.4 33.2 - - + -
94H THR* 5.0 1.3 - - + -
104H CYS* 3.5 31.2 - - + -
105H ARG 4.0 6.5 - - - +
106H TRP* 3.9 36.0 - - + +
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Residues in contact with VAL 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H PHE* 4.5 1.1 - - + +
19H LEU* 1.3 79.4 - - - +
21H VAL* 1.3 65.7 + - - +
22H GLU 3.9 0.2 + - - -
31H TRP* 3.5 45.8 - - + -
32H ASN 3.7 13.0 - - - +
33H GLN* 4.8 4.7 - - + +
104H CYS* 3.3 2.3 - - - -
105H ARG* 2.9 46.8 + - + +
107H VAL* 5.0 3.1 - - + -
112H ILE* 3.6 37.0 - - + -
123H VAL* 5.3 3.4 - - + -
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Residues in contact with VAL 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LEU 4.3 0.4 - - - -
20H VAL* 1.3 74.9 - - - +
22H GLU* 1.3 60.9 + - - +
23H GLU* 4.2 2.7 - - - +
30H LEU 3.5 1.9 - - - +
31H TRP* 3.5 1.4 - - - -
32H ASN* 2.8 49.0 + - + +
33H GLN 3.8 9.1 - - - +
34H PRO* 4.1 4.3 - - + -
55H GLU* 3.4 50.3 - - + +
56H THR* 3.6 14.8 - - + -
101H ILE* 4.3 17.9 - - + -
103H CYS 3.8 3.1 - - - +
104H CYS* 3.6 15.9 - - - -
157H SO4 4.5 2.7 - - - +
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Residues in contact with GLU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H VAL 3.9 0.4 + - - -
21H VAL* 1.3 71.2 - - - +
23H GLU* 1.3 62.3 + - - +
29H ALA* 3.6 30.7 - - + +
30H LEU 3.4 4.7 - - - +
31H TRP* 2.6 37.6 + - + -
101H ILE* 3.8 3.2 - - - +
102H ASP* 2.9 33.7 + - + +
103H CYS* 2.8 30.3 + - - +
105H ARG* 3.5 32.1 + - + -
117H ASN* 4.8 0.6 + - - -
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Residues in contact with GLU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H VAL* 4.6 3.8 - - - +
22H GLU* 1.3 75.4 - - - +
24H THR* 1.3 61.6 + - - +
29H ALA* 4.2 0.7 - - - -
30H LEU* 2.6 48.4 + - - +
32H ASN* 3.8 22.3 + - - +
100H ASP* 3.4 25.1 - - + +
101H ILE* 3.1 22.8 - - + +
102H ASP* 4.1 5.8 - - - -
119H ARG* 3.4 29.5 + - - +
157H SO4 3.1 23.8 + - - -
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Residues in contact with THR 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H GLU* 1.3 74.9 - - - +
25H ILE* 1.3 61.1 - - - +
26H ASN* 4.5 0.4 - - - -
27H GLY* 3.5 14.8 - - - +
28H LYS 3.3 36.8 - - - +
29H ALA* 3.6 7.0 - - + +
30H LEU* 5.6 0.2 - - - -
100H ASP 4.2 4.3 + - - +
102H ASP* 3.0 24.7 + - - +
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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