Contacts of the strand formed by residues 37 - 41 (chain U) 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 SER 37 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36U ASN* 1.3 74.6 - - - +
38U LEU* 1.3 65.6 + - - +
49U ILE 3.0 13.5 - - - -
50U SER* 4.0 13.0 - - - -
77U VAL* 4.1 21.6 - - - +
79U ASN* 2.7 29.2 + - - +
137U THR* 4.8 1.4 + - - -
164U ALA* 3.3 5.2 - - - +
165U THR* 3.0 32.2 + - - +
172U ILE* 4.5 1.2 - - - +
197U MET* 4.2 5.3 - - - +
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Residues in contact with LEU 38 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U SER* 1.3 78.9 - - - +
39U ALA* 1.3 65.8 + - - +
40U VAL* 3.7 32.3 - - + +
47U VAL 3.9 0.2 - - - +
48U VAL* 3.3 4.0 - - - +
49U ILE* 2.8 40.3 + - + +
163U THR* 3.2 13.0 - - - +
164U ALA* 4.0 0.9 - - - +
172U ILE* 3.9 27.8 - - + -
176U LEU* 4.3 10.5 - - + -
193U ALA* 3.7 29.4 - - + +
196U HIS* 4.9 2.2 - - + -
197U MET* 3.9 23.1 - - + +
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Residues in contact with ALA 39 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U LEU* 1.3 75.6 - - - +
40U VAL* 1.3 64.1 + - - +
47U VAL 3.2 4.3 - - - +
48U VAL* 3.5 21.8 - - + -
77U VAL* 6.2 0.2 - - + -
137U THR* 4.3 4.7 - - + -
148U ILE* 3.9 32.8 - - + -
162U ALA* 3.2 6.8 - - - +
163U THR* 2.8 40.0 + - + +
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Residues in contact with VAL 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U LEU* 3.7 13.7 - - + -
39U ALA* 1.3 80.1 - - - +
41U ARG* 1.3 64.4 + - - +
42U GLY 4.2 0.2 + - - -
46U THR* 3.5 4.9 - - - +
47U VAL* 2.9 35.6 + - + +
148U ILE* 3.9 3.4 - - - -
162U ALA* 3.9 16.6 - - + -
176U LEU* 4.1 15.0 - - + -
179U PHE* 5.0 3.6 - - - -
180U ILE* 4.4 11.9 - - - -
189U VAL* 4.0 19.1 - - + +
192U PHE* 4.3 11.7 - - + -
193U ALA* 3.9 26.5 - - + -
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Residues in contact with ARG 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O MET* 4.2 19.5 - - - +
40U VAL* 1.3 75.0 - - - +
42U GLY* 1.3 55.6 + - - +
45U CYS 3.8 3.8 - - - -
46U THR* 4.4 2.0 - - - +
144U LEU 5.8 1.0 + - - -
146U PRO* 3.4 45.3 + - + +
147U SER* 4.2 2.9 - - - +
148U ILE* 3.4 22.2 - - + -
160U TYR 4.1 7.8 + - - -
161U LYS* 3.3 28.4 + - - +
179U PHE* 5.9 1.2 - - - -
180U ILE* 2.8 99.3 + - + +
189U VAL* 4.6 0.9 - - - -
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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