Contacts of the strand formed by residues 37 - 41 (chain Q) in PDB entry 3TDD
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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36Q CYS* 1.3 77.1 - - - +
38Q VAL* 1.3 61.0 + - - +
49Q GLY 3.4 8.7 - - - +
50Q CYS* 4.3 11.2 - - + -
77Q SER* 4.4 6.1 - - - +
78Q PHE 4.0 11.9 - - - +
79Q SER* 3.6 15.3 - - - +
137Q LEU* 4.1 9.4 - - + +
164Q THR* 2.8 17.9 + - - -
165Q ILE* 2.8 30.5 + - + +
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Residues in contact with VAL 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q ALA* 1.3 76.2 - - - +
39Q GLY* 1.3 68.0 + - - +
40Q VAL* 4.3 6.5 - - + -
48Q LEU* 3.4 5.5 - - - +
49Q GLY 2.8 41.0 + - - +
77Q SER* 5.2 0.5 + - - -
137Q LEU* 3.7 6.6 - - - +
163Q GLN 3.3 13.7 - - - +
164Q THR* 4.0 7.9 - - - +
172Q VAL* 4.6 2.5 - - + -
176Q LEU* 3.8 24.0 - - + -
193Q THR* 3.8 17.0 - - + -
196Q SER* 4.1 11.2 - - - +
197Q LEU* 3.8 29.4 - - + -
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Residues in contact with GLY 39 (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* 1.3 76.2 - - - +
40Q VAL* 1.3 64.0 + - - +
47Q VAL 3.1 11.0 - - - -
48Q LEU* 3.7 13.5 - - - -
137Q LEU* 3.8 4.7 - - - +
148Q LEU* 3.2 13.0 - - - +
162Q ALA* 3.1 4.0 - - - -
163Q GLN 2.8 36.9 + - - -
193Q THR* 5.8 0.2 - - - -
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Residues in contact with VAL 40 (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* 4.3 7.9 - - + -
39Q GLY* 1.3 79.5 - - - +
41Q LYS* 1.3 59.7 + - - +
46Q VAL* 4.2 3.5 - - - +
47Q VAL* 2.9 30.1 + - + -
148Q LEU* 4.6 0.2 - - - -
161Q SER 3.8 4.3 - - - -
162Q ALA* 3.5 18.8 - - + -
176Q LEU* 3.7 21.8 - - + -
180Q TYR* 4.6 9.4 - - + -
189Q CYS* 3.4 25.5 - - - +
192Q LEU* 5.1 6.5 - - + -
193Q THR* 2.8 33.7 - - - +
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Residues in contact with LYS 41 (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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40Q VAL* 1.3 72.8 - - - +
42Q GLY* 1.3 65.1 + - - +
45Q CYS 3.5 8.3 - - - +
46Q VAL* 4.0 15.9 - - + +
145Q GLU* 5.2 4.8 + - - +
146Q PRO* 3.0 34.3 + - + -
147Q LYS* 4.1 7.5 - - - +
148Q LEU* 3.7 13.1 + - + +
159Q SER* 5.5 1.2 - - - -
160Q TRP 3.0 22.3 + - - +
161Q SER* 2.9 29.0 + - - +
180Q TYR* 2.7 34.6 + - - +
182Q PRO* 4.1 1.4 - - - +
183Q PRO* 4.2 0.7 - - - +
189Q CYS* 4.2 1.8 - - - -
60R GLU* 3.0 25.0 + - - -
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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