Contacts of the strand formed by residues 46 - 51 (chain Q) 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 VAL 46 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40Q VAL 3.4 15.3 - - - +
41Q LYS* 3.8 10.8 - - + -
42Q GLY 4.4 0.2 - - - +
45Q CYS* 1.3 81.1 - - - +
47Q VAL* 1.3 70.5 + - - +
48Q LEU* 4.4 0.9 - - + -
139Q ALA* 3.8 21.8 - - + -
140Q GLY 4.4 4.3 - - - +
141Q PHE* 4.4 6.5 - - + -
146Q PRO* 3.5 20.4 - - + -
147Q LYS 3.5 22.0 - - - +
148Q LEU* 4.1 11.4 - - + -
214Q VAL* 4.1 0.2 - - - -
215Q VAL* 3.1 42.4 + - + +
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Residues in contact with VAL 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Q GLY* 3.2 5.0 - - - -
40Q VAL 2.8 36.1 + - - +
45Q CYS* 4.6 5.6 - - - -
46Q VAL* 1.3 78.8 - - - +
48Q LEU* 1.3 65.5 + - - +
186Q VAL 4.7 0.9 - - - +
189Q CYS* 3.6 33.7 - - + -
190Q VAL* 4.2 13.0 - - + -
193Q THR* 3.9 27.1 + - + +
212Q ILE* 3.5 30.7 - - + -
213Q THR 3.6 5.6 - - - +
214Q VAL* 4.6 8.5 - - + -
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Residues in contact with LEU 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q VAL 3.4 4.5 - - - +
39Q GLY* 3.8 14.8 - - - -
46Q VAL* 4.4 1.3 - - + -
47Q VAL* 1.3 87.9 - - - +
49Q GLY* 1.3 58.7 + - - +
50Q CYS* 5.2 1.3 - - - -
67Q VAL* 4.1 26.4 - - + +
75Q VAL* 4.1 22.4 - - + +
77Q SER* 4.0 26.0 - - - +
137Q LEU* 4.9 4.7 - - + +
139Q ALA* 3.7 32.5 - - + -
148Q LEU* 3.9 9.9 - - + -
211Q GLU 3.9 0.3 - - - +
212Q ILE* 3.5 4.2 - - - +
213Q THR* 3.0 40.1 + - - +
215Q VAL* 5.0 3.4 - - + -
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Residues in contact with GLY 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q ALA* 3.3 2.3 - - - -
38Q VAL* 2.7 46.3 + - - +
47Q VAL 4.3 0.2 - - - -
48Q LEU* 1.3 74.3 - - - +
50Q CYS* 1.3 63.7 + - - -
193Q THR* 4.3 1.6 - - - +
197Q LEU* 3.8 12.7 - - - +
211Q GLU 3.3 10.3 - - - -
212Q ILE* 3.8 12.8 - - - -
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Residues in contact with CYS 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Q CYS 3.5 9.2 - - - +
37Q ALA* 4.0 15.5 - - + +
38Q VAL 5.6 0.2 - - - -
49Q GLY* 1.3 80.6 - - - -
51Q GLU* 1.3 65.2 - - - +
52Q ARG* 5.0 0.2 - - - +
66Q LYS* 3.8 35.2 - - + -
67Q VAL* 4.0 21.8 - - - -
77Q SER* 4.1 10.1 - - - -
197Q LEU* 4.0 6.3 - - - +
209Q ASN 3.6 0.3 - - - +
210Q ILE* 3.8 0.5 - - - -
211Q GLU* 3.1 42.0 + - + +
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Residues in contact with GLU 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q THR* 3.6 17.1 + - - -
36Q CYS* 3.1 50.0 + - + +
50Q CYS* 1.3 77.7 - - - +
52Q ARG* 1.3 68.3 - - - +
66Q LYS* 5.2 5.0 - - - +
167Q ARG* 3.1 42.9 + - - +
197Q LEU* 4.0 8.4 - - + +
200Q VAL* 4.2 12.6 - - - +
201Q VAL* 3.7 30.3 - - + +
209Q ASN* 3.3 10.9 - - - +
210Q ILE* 4.9 0.2 - - - +
211Q GLU* 6.2 0.2 - - - -
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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