Contacts of the strand formed by residues 107 - 112 (chain C) in PDB entry 3Q29
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 TYR 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C ILE* 3.4 40.8 - - + +
81C THR 4.2 3.8 + - - -
82C PRO* 4.3 5.2 - - + -
86C PHE* 3.8 20.4 - + - -
95C TRP* 4.0 7.2 - + - -
98C VAL* 4.4 0.2 - - - -
106C ALA* 1.3 71.9 - - - +
108C PRO* 1.3 66.1 - - + +
109C ILE* 3.8 2.8 + - + +
264C SER* 3.2 3.3 - - - -
265C ALA* 2.7 48.1 + - + +
267C ILE* 4.2 7.4 - - + -
278C LYS* 3.2 18.6 - - + +
281C LEU* 3.5 34.1 - - + -
282C GLU* 2.5 45.3 + - + -
286C LEU* 4.1 15.3 - - + -
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Residues in contact with PRO 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LEU* 3.4 26.8 - - + +
94C THR* 3.5 47.6 - - - +
95C TRP* 3.5 18.2 - - + -
98C VAL* 4.0 5.6 - - + -
106C ALA 3.8 2.0 - - - +
107C TYR* 1.3 86.1 - - + +
109C ILE* 1.3 60.4 + - - +
262C VAL* 3.9 10.1 - - + -
263C LEU 3.8 4.5 - - - +
264C SER* 4.0 4.9 - - - +
286C LEU* 3.7 13.9 - - - +
304C ALA* 3.5 9.2 - - - +
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Residues in contact with ILE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PHE* 3.8 20.6 - - + -
107C TYR* 4.0 11.2 - - + +
108C PRO* 1.3 81.0 - - - +
110C ALA* 1.3 56.0 + - - +
263C LEU* 2.6 30.0 + - + +
264C SER* 4.1 1.6 - - - -
265C ALA* 4.3 5.2 - - + +
281C LEU* 5.4 0.4 - - + -
285C LEU* 3.5 29.4 - - + -
286C LEU* 4.0 18.0 - - + +
291C LEU* 3.9 22.7 - - + +
300C LEU* 4.2 22.2 - - + -
303C VAL* 3.4 5.5 - - - +
304C ALA* 2.7 27.5 + - - +
305C LEU 4.6 0.7 + - - -
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ILE* 1.3 85.8 - - + +
111C VAL* 1.3 64.6 + - - +
112C GLU* 3.7 0.9 + - - +
262C VAL* 3.3 6.7 - - - +
263C LEU* 2.9 31.3 + - + +
300C LEU* 3.5 40.8 - - + +
302C ALA 3.5 6.1 - - - +
303C VAL* 3.6 13.2 - - + +
304C ALA* 3.9 2.8 - - - +
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C PHE* 3.9 26.9 - - + -
94C THR* 4.1 16.6 - - + -
110C ALA* 1.3 72.8 - - - +
112C GLU* 1.3 64.9 + - - +
113C ALA 4.3 0.2 + - - -
260C VAL* 3.7 26.0 - - + -
261C GLY 3.5 2.7 - - - -
262C VAL* 4.3 5.6 - - + +
301C GLY* 3.6 5.7 - - - -
302C ALA* 2.7 49.7 + - + +
321C THR* 4.4 5.5 - - + +
325C ALA* 4.7 11.9 - - + -
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS* 3.2 22.9 - - - -
64C ALA* 4.9 4.6 - - - +
110C ALA 4.3 4.5 - - - +
111C VAL* 1.3 77.7 - - - +
113C ALA* 1.3 63.9 + - - +
156C TYR* 4.5 6.3 + - - +
230C PRO* 5.0 4.0 - - + -
231C TRP* 3.6 21.6 - - + -
259C PHE 4.1 0.3 - - - +
260C VAL* 3.5 6.8 - - - +
261C GLY* 2.6 39.8 + - - +
263C LEU* 3.4 27.2 - - + +
300C LEU 3.8 17.7 - - - +
321C THR* 4.8 1.3 - - - -
1D GLC 2.7 31.0 + - - -
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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