Contacts of the strand formed by residues 44 - 48 (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 LEU 44 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.3 15.3 - - + -
22A CYS 3.4 2.5 - - - +
23A VAL* 4.3 15.7 - - + -
42A PRO* 3.8 6.5 + - + +
43A VAL* 1.3 82.3 - - - +
45A PHE* 1.3 57.4 + - - +
175A TYR* 3.6 31.4 - - + -
176A VAL* 3.8 36.3 - - + -
179A ILE* 4.0 15.0 - - + -
180A ILE* 5.2 3.6 - - + -
118B PRO* 3.2 14.6 - - - +
120B THR* 2.7 37.0 + - + -
121B LEU* 4.3 12.1 - - + +
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Residues in contact with PHE 45 (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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21A VAL* 3.7 2.6 - - - +
22A CYS* 2.8 73.3 + - + +
23A VAL 3.8 14.1 - - - -
24A GLY* 4.4 4.5 - - - -
43A VAL* 5.3 0.2 - - + -
44A LEU* 1.3 75.7 - - - +
46A LEU* 1.3 72.9 + - - +
47A LYS* 4.3 4.0 - - + -
102A ASP* 3.6 14.1 - - - -
119A TRP* 3.9 26.9 - + + -
123A LYS* 3.5 56.3 - - + -
124A SER* 4.8 0.2 - - - -
118B PRO* 3.9 15.7 - - + -
120B THR* 3.5 7.4 - - - +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 6.2 0.7 - - + -
20A ILE 3.4 6.1 - - - +
21A VAL* 3.6 31.4 - - + -
45A PHE* 1.3 84.3 - - - +
47A LYS* 1.3 62.3 + - - +
124A SER* 2.6 28.9 + - - -
180A ILE* 4.1 15.0 - - + -
46B LEU* 3.5 44.1 - - + +
47B LYS 4.4 0.4 - - - -
48B PRO* 4.2 17.0 - - + -
120B THR* 4.3 10.7 + - + +
124B SER* 3.6 20.9 - - - +
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Residues in contact with LYS 47 (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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18A LYS 5.2 0.2 - - - +
19A ASN* 4.6 1.0 - - - -
20A ILE* 3.1 35.7 + - + +
22A CYS* 3.7 25.6 - - - -
45A PHE* 4.3 3.1 - - + -
46A LEU* 1.3 79.1 - - - +
48A PRO* 1.3 77.6 - - + +
49A SER 4.0 0.2 + - - -
51A ALA* 3.9 3.6 - - + -
102A ASP* 2.9 33.3 + - - +
103A MET 3.5 5.3 + - - -
123A LYS 2.7 31.2 + - - +
124A SER* 4.1 0.7 - - - -
128A SER* 2.8 34.2 + - - +
129A CYS* 3.9 18.2 - - + -
189A LEU* 4.5 2.9 - - - -
46B LEU* 4.1 3.1 - - - -
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Residues in contact with PRO 48 (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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18A LYS 4.7 0.2 - - - -
20A ILE* 3.4 6.4 - - - +
47A LYS* 1.3 92.2 - - + +
49A SER* 1.3 65.9 + - - +
50A THR* 3.9 14.1 - - - +
51A ALA* 3.1 22.7 + - + +
124A SER 3.1 29.8 - - - +
125A PHE 5.0 0.9 - - - +
19B ASN* 3.4 21.8 - - + +
21B VAL* 6.1 0.4 - - + -
46B LEU* 3.8 17.0 - - + -
180B ILE* 3.6 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