Contacts of the strand formed by residues 303 - 308 (chain E) in PDB entry 5MQF
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 LEU 303 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E LEU* 3.3 2.8 - - - +
297E PHE* 2.5 48.7 + - + +
300E SER* 4.9 3.2 - - - -
301E GLY 3.5 0.8 - - - -
302E HIS* 1.3 77.0 - - - +
304E LEU* 1.3 57.7 + - - +
316E TRP 3.5 10.1 - - - +
317E GLU* 4.6 4.9 - - + +
325E LEU* 6.1 1.8 - - + -
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Residues in contact with LEU 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E ARG 3.3 14.1 - - - +
296E LEU* 3.8 6.7 - - + +
301E GLY 5.9 0.9 - - - +
302E HIS 3.5 2.2 + - - -
303E LEU* 1.3 74.1 - - - +
305E LEU* 1.3 60.1 + - - +
306E SER* 3.9 0.9 - - - -
316E TRP* 2.8 47.1 + - + +
318E VAL* 4.4 17.3 - - + -
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Residues in contact with LEU 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E ALA 4.2 0.3 - - - +
295E ARG* 2.9 53.5 + - + +
296E LEU* 4.1 1.7 - - - +
303E LEU 4.3 0.4 - - - -
304E LEU* 1.3 70.9 - - - +
306E SER* 1.3 62.1 + - - +
307E CYS* 3.8 2.4 + - - +
314E LYS 3.7 7.0 - - - +
315E LEU* 4.9 3.6 - - - +
316E TRP 4.7 0.7 - - - +
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Residues in contact with SER 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E VAL* 6.3 1.8 - - - -
293E ALA 4.0 4.0 - - - -
294E VAL* 5.2 1.6 - - - +
295E ARG 5.1 0.2 - - - +
304E LEU* 3.8 2.3 + - - -
305E LEU* 1.3 72.9 - - - +
307E CYS* 1.3 61.2 + - - +
308E SER* 4.1 1.0 + - - -
313E ILE* 4.3 0.3 - - - -
314E LYS* 2.9 49.1 + - - +
316E TRP* 5.2 7.9 - - - -
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Residues in contact with CYS 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E VAL* 3.2 6.9 - - - +
292E SER* 2.4 33.0 + - - -
293E ALA* 2.9 40.8 + - + +
305E LEU 3.8 1.9 + - - +
306E SER* 1.3 72.8 - - - +
308E SER* 1.3 53.7 - - - +
312E LYS 5.0 2.2 - - - -
313E ILE* 5.2 6.3 - - + +
314E LYS 5.0 0.2 - - - +
335E VAL* 4.8 13.0 - - + -
338E ILE* 4.7 11.2 - - + -
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Residues in contact with SER 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E HIS* 3.8 29.4 - - - -
289E LYS 4.3 2.2 - - - -
290E GLY 3.3 10.3 - - - -
291E VAL* 3.9 3.1 - - - +
292E SER* 3.3 11.3 - - - +
306E SER* 4.1 2.1 + - - -
307E CYS* 1.3 75.1 - - - +
309E MET* 1.3 64.6 + - - +
310E ASP* 3.1 13.8 + - - -
311E CYS* 3.4 11.1 + - - -
312E LYS 4.3 13.1 + - - -
314E LYS* 6.2 2.7 - - - -
335E VAL* 4.5 6.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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