Contacts of the strand formed by residues 99 - 104 (chain E) in PDB entry 1SID
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 99 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53E LEU* 4.2 5.3 - - - +
54E ASN 4.2 10.8 - - - -
55E PRO* 4.1 4.2 - - - +
56E ARG* 3.4 32.2 + - - +
97E THR 3.4 11.2 + - - -
98E TRP* 1.3 74.4 - - - +
100E MET* 1.3 62.8 + - - +
219E ASP* 3.6 5.4 - - - -
220E GLY* 4.5 0.7 - - - +
281E SER* 3.4 0.7 - - - -
282E CYS* 2.9 49.2 + - - -
283E VAL* 4.7 3.8 - - - +
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Residues in contact with MET 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LEU* 4.4 8.3 - - - +
56E ARG* 3.8 6.0 + - - +
98E TRP 5.3 0.2 - - - +
99E SER* 1.3 74.9 - - - +
101E ALA* 1.3 85.4 + - - +
102E LYS* 4.8 3.1 - - + +
171E PRO* 5.2 0.4 - - + -
216E LEU* 3.4 42.4 - - + +
217E ASP 4.8 4.7 - - - +
218E LYS 3.5 20.9 - - - +
219E ASP* 3.0 36.7 + - + +
279E TYR* 4.3 22.7 - - + -
280E LEU 3.3 16.8 - - - +
281E SER* 4.0 2.7 - - - +
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E LEU* 4.3 18.6 - - + -
100E MET* 1.3 93.8 - - - +
102E LYS* 1.3 65.6 + - - +
103E LEU* 4.2 7.7 - - + +
278E LEU 3.6 1.2 - - - +
279E TYR* 3.6 2.9 - - - -
280E LEU* 3.1 28.6 + - + +
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Residues in contact with LYS 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E MET* 4.8 4.0 - - + +
101E ALA* 1.3 78.3 - - - +
103E LEU* 1.3 74.4 + - - +
104E GLN* 3.6 22.9 + - + +
277E GLY* 4.2 5.6 - - - -
278E LEU 3.2 13.2 - - - +
279E TYR* 3.3 41.8 + - + +
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E MET* 3.9 27.1 - - + -
49E ILE* 4.6 16.2 - - + -
51E ALA* 5.0 10.5 - - + -
53E LEU* 6.4 0.2 - - + -
101E ALA* 4.6 6.7 - - + +
102E LYS* 1.3 82.4 - - - +
104E GLN* 1.3 60.8 + - - +
105E LEU* 3.2 10.0 + - + +
277E GLY* 3.7 4.0 - - - -
278E LEU* 2.8 59.0 + - + +
280E LEU* 4.0 26.0 - - + -
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Residues in contact with GLN 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E MET* 3.9 18.0 - - - +
37E LEU* 4.8 2.1 - - - +
102E LYS* 3.6 25.2 + - + +
103E LEU* 1.3 73.3 - - - +
105E LEU* 1.3 83.5 + - - +
106E PRO* 4.0 1.4 - - - +
276E GLU* 2.6 46.9 + - - +
277E GLY* 4.5 1.0 + - - -
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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