Contacts of the strand formed by residues 258 - 266 (chain C) in PDB entry 3IOT
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 PHE 258 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLU 3.8 7.6 - - - +
112C ALA* 3.9 12.1 - - - +
113C LEU* 4.5 0.6 + - - +
155C TYR* 3.8 32.5 + + + +
158C TRP* 3.5 35.5 - + - -
159C PRO* 5.2 0.8 - - - +
168C ALA* 4.7 6.7 - - + -
257C PRO* 1.3 81.4 - - - +
259C VAL* 1.3 60.9 + - - +
260C GLY 4.1 0.4 - - - -
328C GLU* 3.2 24.2 - - + -
330C MET* 3.4 26.7 - - + -
331C PRO* 4.4 12.6 - - + -
336C MET* 3.5 23.1 - - + -
339C PHE* 4.7 5.6 - + - -
340C TRP* 3.2 40.8 - + - -
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Residues in contact with VAL 259 (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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64C HIS* 3.1 19.9 + - - -
92C PHE* 4.9 7.6 - - + -
110C VAL* 3.6 30.7 - - + -
111C GLU 3.4 4.5 - - - +
112C ALA* 4.8 0.4 - - + -
257C PRO 3.9 2.0 - - - +
258C PHE* 1.3 79.0 - - - +
260C GLY* 1.3 60.2 + - - +
261C VAL* 3.7 14.1 + - + +
324C ALA* 3.6 32.5 - - + +
328C GLU 3.0 29.2 + - - +
329C ILE* 4.0 13.7 - - + +
330C MET* 3.6 11.0 + - - +
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Residues in contact with GLY 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ALA* 5.6 6.3 - - - -
64C HIS* 4.1 6.3 - - - -
65C ASP* 5.7 0.9 - - - -
109C ALA 3.8 1.0 - - - +
110C VAL 3.7 0.5 - - - -
111C GLU* 2.8 49.5 + - - +
155C TYR* 5.4 2.8 + - - -
258C PHE 4.1 1.2 - - - -
259C VAL* 1.3 70.7 - - - +
261C VAL* 1.3 60.0 + - - -
262C LEU 4.1 0.3 + - - -
330C MET* 4.7 9.9 - - - +
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Residues in contact with VAL 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ALA* 4.3 3.1 - - - +
64C HIS* 2.7 49.2 + - + +
92C PHE* 5.3 2.5 - - + -
93C THR* 5.2 7.0 - - + +
96C ALA* 4.5 19.1 - - + -
97C VAL* 5.5 0.2 - - + -
107C PRO* 4.3 18.8 - - + -
108C ILE 4.4 0.2 - - - +
109C ALA 3.2 13.5 - - - +
110C VAL* 4.3 15.0 - - + -
259C VAL* 3.8 24.9 - - + +
260C GLY* 1.3 75.7 - - - +
262C LEU* 1.3 71.2 + - - +
263C SER* 4.0 6.3 - - - +
303C ALA* 6.0 0.2 - - + -
329C ILE* 6.0 0.7 - - + -
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Residues in contact with LEU 262 (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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11C ILE* 5.0 5.4 - - + -
15C LYS* 4.5 28.9 - - + +
61C PHE* 4.0 18.2 - - + +
62C TRP* 3.7 34.1 - - + +
63C ALA* 4.0 4.5 - - - +
108C ILE* 2.7 54.4 + - + -
109C ALA* 2.9 21.5 + - + +
260C GLY 4.1 1.2 + - - -
261C VAL* 1.3 73.8 - - - +
263C SER* 1.3 58.3 + - - +
299C LEU* 4.8 13.7 - - + -
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Residues in contact with SER 263 (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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60C ILE 3.2 2.3 - - - +
61C PHE* 3.1 6.4 - - - -
62C TRP 2.9 31.4 + - - +
64C HIS* 3.6 7.4 - - - +
67C PHE* 3.5 21.5 - - - -
97C VAL* 3.4 18.0 - - - +
105C ALA* 3.9 10.1 - - - -
106C TYR 3.2 10.1 - - - -
107C PRO* 4.4 0.2 - - - +
108C ILE* 4.1 4.9 - - - -
261C VAL* 3.3 12.6 + - - +
262C LEU* 1.3 79.5 + - - +
264C ALA* 1.3 60.7 + - - +
265C GLY 3.9 0.2 - - - -
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Residues in contact with ALA 264 (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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59C ILE* 4.9 1.3 - - + -
60C ILE 3.5 4.7 - - - -
61C PHE* 3.6 33.7 - - + -
79C ILE* 5.5 0.7 - - - +
105C ALA* 3.2 4.7 - - - -
106C TYR* 2.8 46.7 + - + +
108C ILE* 4.0 4.9 - - + +
263C SER* 1.3 70.5 - - - +
265C GLY* 1.3 61.6 + - - +
266C ILE* 4.4 0.9 + - - +
280C LEU* 4.0 23.9 - - + +
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Residues in contact with GLY 265 (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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59C ILE* 3.1 7.5 - - - +
60C ILE* 2.8 40.2 + - - +
67C PHE* 3.6 19.8 - - - -
76C LEU* 4.3 5.8 - - - -
104C ILE 4.2 4.9 - - - -
105C ALA* 4.0 6.1 - - - -
264C ALA* 1.3 75.1 - - - +
266C ILE* 1.3 62.2 + - - -
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Residues in contact with ILE 266 (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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58C ASP 3.5 8.7 - - - +
59C ILE* 3.8 15.7 - - + -
76C LEU* 3.4 8.2 - - - +
77C ALA* 2.8 48.1 + - + +
79C ILE* 4.2 23.9 - - + +
104C ILE 4.8 2.6 + - - -
105C ALA* 5.6 0.4 - - - +
106C TYR* 4.8 1.6 - - + -
264C ALA 5.3 0.7 - - - +
265C GLY* 1.3 74.9 - - - -
267C ASN* 1.3 69.1 + - - +
270C SER* 4.6 3.8 - - - -
273C LYS* 4.4 20.0 - - + +
276C ALA* 3.7 23.8 - - + -
277C LYS* 4.1 16.2 - - + +
280C LEU* 4.5 9.0 - - + -
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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