Contacts of the strand formed by residues 37 - 41 (chain R) in PDB entry 3SDI
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 ALA 37 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R THR* 1.3 77.1 - - - +
38R ILE* 1.3 63.7 + - - +
49R GLY 3.5 4.7 - - - +
50R VAL* 4.0 11.4 - - + -
77R ALA* 4.2 5.8 - - + -
78R MET 3.9 20.4 - - - +
79R SER* 4.5 0.7 - - - -
137R LEU* 3.6 10.4 - - + +
164R ALA* 3.2 2.9 - - - -
165R ILE* 2.8 53.7 + - + +
197R LEU* 5.4 0.2 - - - -
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Residues in contact with ILE 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R THR* 4.2 12.1 - - + -
37R ALA* 1.3 78.6 - - - +
39R GLY* 1.3 63.8 + - - +
40R ILE* 4.5 5.6 - - + -
47R VAL 3.9 0.2 - - - +
48R LEU* 3.4 2.4 - - - +
49R GLY 2.8 40.8 + - - +
137R LEU* 3.8 5.0 - - - +
163R LYS 3.4 9.4 - - - +
164R ALA* 4.0 11.7 - - + -
172R ALA* 4.6 1.6 - - + -
176R LEU* 4.1 25.4 - - + -
193R VAL* 4.2 19.1 - - + +
196R ILE* 3.8 32.8 - - + +
197R LEU* 3.7 31.4 - - + +
200R VAL* 5.1 0.2 - - + -
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Residues in contact with GLY 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ILE* 1.3 75.0 - - - +
40R ILE* 1.3 65.6 + - - +
47R VAL 3.1 10.3 - - - -
48R LEU* 3.9 9.4 - - - -
137R LEU* 3.7 5.0 - - - +
148R LEU* 3.3 18.4 - - - +
162R ALA* 3.4 1.7 - - - +
163R LYS 2.9 34.6 + - - +
193R VAL* 5.5 0.2 - - - -
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Residues in contact with ILE 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R ILE* 4.5 1.6 - - + -
39R GLY* 1.3 77.8 - - - +
41R ALA* 1.3 63.1 + - - +
42R THR* 4.0 4.6 + - + +
45R GLY 4.2 0.3 - - - +
46R VAL* 3.2 6.1 - - - +
47R VAL* 2.8 41.0 + - + +
148R LEU* 4.1 0.8 - - - +
161R ASN 3.8 2.9 - - - -
162R ALA* 4.5 0.2 - - - +
176R LEU* 3.9 22.4 - - + -
180R TRP* 3.9 25.4 - - + +
184R LEU* 4.7 4.5 - - + -
189R ALA* 3.5 31.2 - - + +
192R LEU* 3.8 25.8 - - + -
193R VAL* 3.4 31.2 - - + +
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Residues in contact with ALA 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R ILE* 1.3 73.2 - - - +
42R THR* 1.3 63.9 + - - +
46R VAL* 3.9 19.7 - - + -
146R TYR 5.0 3.6 - - - +
147R GLN* 4.7 3.6 - - - -
148R LEU* 4.2 19.9 - - + +
160R TYR 4.3 4.7 - - - +
161R ASN* 2.8 23.7 + - - +
180R TRP* 3.3 27.5 + - - -
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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