Contacts of the strand formed by residues 213 - 220 (chain A) in PDB entry 1SAW
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 VAL 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LEU* 4.2 6.7 - - + -
132A SER* 4.0 28.9 - - - +
133A ALA* 4.4 16.4 - - + +
135A VAL* 4.1 20.0 - - + -
149A TRP* 5.0 0.7 - - - -
208A GLY* 3.1 2.4 - - - -
209A ILE* 2.9 54.8 + - + +
212A LEU* 1.3 82.9 - - + +
214A SER* 1.3 74.8 + - - +
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Residues in contact with SER 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 3.9 8.1 - - - +
132A SER* 5.0 1.2 - - - -
133A ALA 5.6 0.7 + - - -
149A TRP* 4.4 15.9 - - - -
206A GLU* 5.8 2.9 - - - -
207A ALA 3.3 11.4 - - - -
208A GLY* 4.0 0.2 - - - -
213A VAL* 1.3 87.3 - - - +
215A MET* 1.3 65.6 + - - +
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Residues in contact with MET 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 3.8 17.7 - - + +
99A LEU* 3.5 39.9 - - + +
100A CYS 4.2 1.6 - - - -
101A LEU* 3.6 39.5 - - + -
130A PRO 4.3 2.9 - - - +
132A SER* 3.5 26.0 - - - -
205A ILE 3.9 0.9 - - - +
206A GLU* 3.4 4.5 - - - +
207A ALA* 2.9 43.9 + - + +
214A SER* 1.3 79.3 - - - +
216A THR* 1.3 63.7 + - - +
217A PHE* 3.7 24.5 - - + -
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Residues in contact with THR 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 3.4 25.7 + - - +
56A GLY 4.7 3.3 + - - -
204A GLU* 3.9 33.2 - - + +
205A ILE 3.5 6.3 - - - +
206A GLU* 3.3 24.9 + - + +
215A MET* 1.3 73.8 - - - +
217A PHE* 1.3 75.7 + - - +
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Residues in contact with PHE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA* 3.1 29.2 - - + -
54A PRO 3.5 5.8 - - - -
55A GLU* 3.7 18.2 - - + -
56A GLY 5.3 0.2 - - - -
57A SER 3.1 27.6 - - - -
58A PRO 4.8 0.2 - - - -
59A ILE* 3.7 25.4 - - + -
101A LEU* 4.5 3.8 - - + -
130A PRO* 3.5 25.4 - - + -
131A VAL 3.5 6.7 - - - -
204A GLU* 3.4 7.6 - - - +
205A ILE* 2.8 39.7 + - + +
215A MET* 3.7 40.6 - - + -
216A THR* 1.3 88.5 - - - +
218A LYS* 1.3 59.9 + - - +
219A VAL 4.2 0.2 - - - -
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A SER 5.3 0.4 + - - -
58A PRO* 3.7 10.4 - - + +
59A ILE* 3.1 22.9 + - - +
202A ASN* 4.3 28.8 + - - +
203A ASP 3.5 9.4 - - - +
204A GLU* 4.5 15.5 - - + +
217A PHE* 1.3 75.6 - - - +
219A VAL* 1.3 72.3 + - - +
220A GLU* 3.5 24.5 + - - +
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 3.7 19.7 - - + +
61A MET* 3.6 28.7 - - + -
199A VAL* 4.0 17.3 - - + -
200A LYS 3.2 27.6 - - - +
201A GLU* 3.9 3.4 - - - -
202A ASN* 3.1 24.9 + - - +
203A ASP* 2.8 15.2 + - + +
205A ILE* 3.6 28.3 - - + -
217A PHE 4.2 0.4 - - - -
218A LYS* 1.3 75.0 - - - +
220A GLU* 1.3 69.0 + - - +
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PRO* 3.5 30.2 - - + +
59A ILE 2.9 14.4 + - - +
60A LEU* 3.4 4.4 - - + +
61A MET* 3.0 28.3 + - - +
201A GLU* 4.7 5.8 - - - -
202A ASN* 5.0 3.8 - - - +
218A LYS* 4.1 30.8 + - - +
219A VAL* 1.3 79.1 - - - +
221A LYS* 1.3 67.2 + - - +
223A GLU* 5.4 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