Contacts of the strand formed by residues 99 - 104 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D LEU* 3.9 7.9 - - - +
54D ASN 4.3 8.7 - - - -
55D PRO* 4.1 5.3 - - - +
56D ARG* 3.4 31.2 + - - +
97D THR 3.6 8.1 + - - -
98D TRP* 1.3 70.9 - - - +
100D MET* 1.3 64.8 + - - +
219D ASP* 4.0 4.9 - - - -
220D GLY* 4.6 1.1 - - - +
281D SER* 3.4 0.7 - - - -
282D CYS* 2.9 50.6 + - - +
283D VAL* 4.6 5.4 - - - -
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Residues in contact with MET 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 4.1 8.4 - - - +
56D ARG* 3.6 16.7 + - - +
98D TRP 5.3 0.2 - - - +
99D SER* 1.3 77.8 - - - +
101D ALA* 1.3 102.2 + - - +
102D LYS* 5.3 2.9 - - + +
171D PRO* 5.4 1.6 - - + -
216D LEU* 3.1 50.9 - - + +
217D ASP* 3.9 8.1 - - - +
218D LYS 3.2 19.1 - - - +
219D ASP* 3.5 18.9 + - + +
279D TYR* 5.0 16.4 - - + -
280D LEU 3.1 15.7 - - - +
281D SER* 3.9 0.7 - - - -
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 4.2 17.9 - - + +
100D MET* 1.3 89.6 - - - +
102D LYS* 1.3 63.3 + - - +
103D LEU* 5.0 5.6 - - + -
278D LEU 3.9 0.2 - - - +
279D TYR* 3.6 3.6 - - - +
280D LEU* 2.9 33.0 + - + +
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Residues in contact with LYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D MET* 4.5 3.6 - - + -
101D ALA* 1.3 77.8 - - - +
103D LEU* 1.3 76.2 + - - +
104D GLN* 3.6 25.2 + - - +
276D GLU 6.0 0.8 - - - +
277D GLY* 4.0 7.6 - - - +
278D LEU 3.3 10.8 - - - +
279D TYR* 3.3 46.2 + - + +
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D MET* 3.9 29.4 - - + -
49D ILE* 4.2 17.5 - - + -
51D ALA* 5.3 10.5 - - + -
53D LEU* 6.5 0.2 - - + -
101D ALA* 5.0 5.8 - - + -
102D LYS* 1.3 82.4 - - - +
104D GLN* 1.3 61.4 + - - +
105D LEU* 3.7 8.2 + - + -
276D GLU 3.6 2.6 - - - +
278D LEU* 2.7 61.6 + - + +
280D LEU* 3.8 25.8 - - + -
308D ILE* 6.3 0.2 - - + -
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Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D MET* 3.3 22.6 - - + +
37D LEU* 3.8 3.3 - - - +
102D LYS* 3.6 25.4 + - - +
103D LEU* 1.3 73.5 - - - +
105D LEU* 1.3 93.9 + - - +
276D GLU* 2.9 35.8 + - - +
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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