Contacts of the strand formed by residues 317 - 328 (chain I) in PDB entry 5BRR
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 317 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I LEU* 4.0 17.9 - - + -
163I LEU* 3.3 19.1 - - + +
164I VAL 6.2 0.2 - - - -
165I LEU* 5.1 4.5 - - + -
287I ARG* 4.9 0.5 + - - -
298I MET* 2.8 20.9 + - + +
299I PHE* 3.4 46.5 - - + +
306I PHE* 3.7 24.2 - - + -
316I HIS* 1.3 72.2 + - - +
318I ALA* 1.3 61.9 + - - +
319I LEU 3.5 26.0 - - - +
320I ALA* 4.0 7.2 - - + -
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Residues in contact with ALA 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I LEU* 6.2 0.7 - - + -
161I THR* 3.9 37.5 - - + +
162I ARG 5.1 0.9 - - - +
163I LEU 3.0 8.8 + - - +
164I VAL* 4.3 0.2 - - + -
287I ARG* 3.8 26.9 + - - +
316I HIS* 3.2 22.4 + - + +
317I VAL* 1.3 74.8 - - - +
319I LEU* 1.3 64.5 + - + +
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Residues in contact with LEU 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I GLY* 3.3 33.7 - - - +
154I THR* 4.0 12.8 - - + -
156I ALA* 4.3 14.8 - - + -
157I VAL* 4.2 16.6 - - + +
161I THR* 5.7 0.4 - - + -
164I VAL* 3.5 22.2 - - + +
165I LEU 3.1 22.1 + - - -
285I ASP* 4.2 10.1 - - - +
287I ARG* 5.5 2.5 - - - -
317I VAL* 3.5 9.0 - - - +
318I ALA* 1.3 84.5 - - + +
320I ALA* 1.3 61.8 + - - +
321I LEU* 3.7 24.9 - - + -
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Residues in contact with ALA 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I LEU* 3.3 31.0 - - + -
285I ASP* 4.2 1.4 + - - +
286I LEU* 3.0 36.8 + - + -
287I ARG* 4.5 3.1 + - - +
290I LEU* 4.9 2.0 - - + -
298I MET* 6.0 0.4 - - + -
299I PHE* 4.3 13.4 - - + -
317I VAL* 4.0 11.8 - - + +
319I LEU* 1.3 74.1 - - - +
321I LEU* 1.3 79.6 + - - +
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Residues in contact with LEU 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I LEU* 3.9 18.4 - - + -
153I GLY* 3.8 22.7 - - - -
154I THR* 5.7 0.7 - - + -
165I LEU* 2.9 11.1 + - - +
166I VAL* 3.7 9.6 - - + +
167I ASN* 3.1 26.0 + - - +
283I GLU* 3.7 23.6 - - + +
284I VAL 3.3 13.5 - - - +
285I ASP* 3.7 18.4 - - + +
286I LEU* 4.2 8.8 - - - +
319I LEU* 3.7 19.3 - - + -
320I ALA* 1.3 118.9 - - - +
322I GLN* 1.3 62.3 + - - +
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Residues in contact with GLN 322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I PHE* 3.2 19.1 - - + -
35I SER* 2.6 36.0 + - - -
39I VAL* 3.4 21.6 - - - +
151I LEU* 6.1 0.4 - - - -
167I ASN* 2.6 36.0 + - + +
169I LEU* 4.6 0.4 - - + -
282I THR 3.8 0.5 - - - +
283I GLU* 3.3 2.4 - - - +
284I VAL* 2.7 41.2 + - + +
286I LEU* 3.8 18.7 - - + +
321I LEU* 1.3 75.2 - - - +
323I LYS* 1.3 63.2 + - - +
324I VAL* 3.0 22.7 - - + +
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Residues in contact with LYS 323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I ILE* 3.7 27.8 - - + +
150I HIS* 3.3 51.6 + - - +
151I LEU* 4.5 14.5 - - + +
152I LEU* 6.0 1.3 - - - -
167I ASN 2.9 9.9 + - - -
168I ALA* 3.2 31.1 - - + +
169I LEU 3.3 4.3 + - - -
281I GLU* 3.4 30.9 + - + +
282I THR 3.3 11.0 - - - +
283I GLU* 3.7 33.2 - - + +
322I GLN* 1.3 72.3 - - - +
324I VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I VAL* 4.0 10.8 - - + +
34I PHE* 3.9 6.5 - - - +
35I SER* 3.7 14.1 - - - +
148I ILE* 4.6 1.6 - - - -
169I LEU* 3.5 9.0 - - + -
280I LEU 3.9 0.2 - - - +
281I GLU* 3.2 7.6 - - - +
282I THR 2.8 32.1 + - - +
322I GLN* 3.0 39.5 - - + +
323I LYS* 1.3 74.6 - - - +
325I LYS* 1.3 66.0 + - - +
326I ILE* 3.4 28.3 - - + -
372I PHE* 3.7 19.5 - - + -
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Residues in contact with LYS 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I MET* 3.9 20.9 + - - +
148I ILE* 4.3 7.9 - - + -
169I LEU 2.9 12.0 + - - +
170I TYR* 3.3 23.6 - - + -
171I PHE 2.7 32.7 + - - +
279I SER* 4.5 6.7 - - - -
280I LEU 3.1 8.3 - - - +
281I GLU* 3.7 38.6 + - + +
324I VAL* 1.3 78.5 - - - +
326I ILE* 1.3 60.2 + - - +
327I GLU* 4.0 24.8 + - - -
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Residues in contact with ILE 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I VAL* 3.1 43.3 - - + -
34I PHE 4.7 0.9 - - - +
171I PHE* 3.3 26.2 - - + -
235I MET* 4.5 10.1 - - + -
278I PHE* 4.9 5.5 - - + -
279I SER* 3.7 0.5 - - - -
280I LEU 2.9 31.8 + - - +
324I VAL* 3.4 13.9 - - + -
325I LYS* 1.3 75.8 - - - +
327I GLU* 1.3 75.0 + - - +
328I VAL* 4.3 4.0 - - + -
360I PHE* 4.1 23.3 - - + -
362I VAL* 5.2 0.4 - - + -
372I PHE* 4.0 23.3 - - + -
373I MET 4.8 0.4 - - - +
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Residues in contact with GLU 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147I MET* 5.6 2.6 - - - +
170I TYR* 3.8 22.1 + - + -
171I PHE* 2.8 10.5 + - - +
172I ASN* 3.2 30.0 + - - +
173I GLY* 3.5 23.9 + - - -
228I TYR* 5.1 0.9 + - - -
278I PHE 3.8 5.0 - - - +
279I SER* 2.8 26.5 + - - +
325I LYS* 4.0 16.2 + - - -
326I ILE* 1.3 78.5 - - - +
328I VAL* 1.3 67.0 + - - +
329I ASN* 5.3 4.5 - - - +
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Residues in contact with VAL 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I GLY 5.5 0.2 - - - +
175I TRP* 3.9 18.4 - - + -
202I MET* 3.7 19.1 - - + -
228I TYR* 4.6 4.3 - - - +
235I MET* 3.7 27.8 - - + -
275I LEU* 4.3 12.3 - - + -
276I PRO 4.5 2.5 - - - +
277I LYS* 3.6 4.2 - - - +
278I PHE* 2.9 71.5 + - + +
326I ILE* 4.3 2.2 - - + -
327I GLU* 1.3 79.3 - - - +
329I ASN* 1.3 65.4 + - - +
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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