Contacts of the strand formed by residues 5107 - 5116 (chain E) in PDB entry 1Y1S
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 VAL5107 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5105E GLY 4.2 7.0 - - - +
5106E ASP* 1.3 75.0 - - - +
5108E LEU* 1.3 64.8 + - - +
5109E VAL* 4.6 2.0 - - + -
5144E ALA* 4.7 1.8 - - + -
5149E ALA* 3.8 16.6 - - + -
5150E THR 2.9 13.8 + - - +
5151E THR* 3.1 18.8 - - + +
5152E HIS 2.9 24.1 + - - -
5216E VAL* 3.5 28.0 - - + -
5217E ALA 3.5 6.1 - - - +
5218E GLY* 5.0 2.9 - - - -
5237E THR 5.5 1.8 - - - +
5240E HIS* 5.2 5.4 - - + -
5241E ALA* 4.9 10.1 - - + +
5244E ILE* 3.7 28.0 - - + -
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Residues in contact with LEU5108 (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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5095E THR* 3.9 11.9 - - + -
5097E ALA* 4.9 0.2 - - + -
5102E ILE* 3.6 27.4 - - + -
5106E ASP 4.2 1.8 - - - +
5107E VAL* 1.3 80.3 - - - +
5109E VAL* 1.3 62.6 + - - +
5110E THR* 4.0 3.5 + - - +
5152E HIS* 3.4 13.2 - - + -
5193E MET* 4.0 27.4 - - + -
5194E ASN* 3.3 44.6 - - + +
5215E MET* 4.0 0.3 - - - +
5216E VAL* 3.2 5.1 - - - -
5217E ALA* 3.0 42.5 + - + +
5219E VAL* 3.6 16.6 - - + -
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Residues in contact with VAL5109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5107E VAL* 4.6 2.5 - - + -
5108E LEU* 1.3 74.4 - - - +
5110E THR* 1.3 63.1 + - - +
5111E THR 3.8 0.2 + - - -
5137E THR* 4.2 15.7 - - + +
5140E LEU* 4.0 29.8 - - + +
5141E VAL* 3.9 28.7 - - + -
5144E ALA* 5.0 0.2 - - + -
5151E THR* 3.6 25.1 - - + -
5152E HIS 2.8 11.4 + - - +
5153E VAL* 3.3 6.7 - - + +
5154E GLY 3.0 25.6 + - - -
5193E MET* 3.2 3.4 - - - +
5215E MET 3.6 10.1 - - - +
5216E VAL* 4.4 12.3 - - + +
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Residues in contact with THR5110 (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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5108E LEU* 4.8 2.8 + - - +
5109E VAL* 1.3 75.2 - - - +
5111E THR* 1.3 65.2 + - - +
5112E ALA 3.5 17.5 - - - +
5113E SER* 3.4 25.1 - - - +
5132E ALA* 3.5 16.8 - - - +
5137E THR* 4.3 3.5 + - - -
5154E GLY 3.4 3.6 - - - -
5156E THR* 2.8 25.6 - - + +
5193E MET* 4.3 0.7 - - - +
5194E ASN* 5.5 0.2 + - - -
5199E SER* 4.8 1.8 - - - +
5203E LEU* 4.1 8.5 - - + -
5215E MET* 2.9 44.3 + - - +
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Residues in contact with THR5111 (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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1131A VAL* 4.0 24.7 - - - +
1132A ALA 4.8 2.5 + - - +
1134A PHE* 4.3 17.9 - - + +
5110E THR* 1.3 74.3 - - - +
5112E ALA* 1.3 64.5 + - - +
5131E VAL* 3.3 7.1 - - - +
5132E ALA* 2.8 28.9 + - - +
5137E THR* 4.4 11.4 - - + -
5153E VAL* 3.6 30.3 - - + -
5154E GLY* 2.8 27.6 + - - +
5155E VAL* 3.9 1.0 + - - +
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Residues in contact with ALA5112 (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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1112A ALA* 5.4 0.2 - - + -
1129A PRO* 3.5 24.5 - - + -
1131A VAL* 3.6 20.6 - - + -
5110E THR* 3.5 4.8 - - - +
5111E THR* 1.3 83.1 + - - +
5113E SER* 1.3 65.6 + - - +
5130E ALA 3.0 15.5 - - - +
5131E VAL* 3.8 6.7 - - + +
5155E VAL* 3.0 26.3 - - - +
5156E THR 3.2 2.1 + - - -
5203E LEU* 4.3 1.1 - - - -
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Residues in contact with SER5113 (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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1127A GLU 4.0 0.2 - - - +
1129A PRO* 3.4 15.7 - - - +
5110E THR* 3.4 9.5 - - - +
5112E ALA* 1.3 72.8 - - - +
5114E VAL* 1.3 63.1 + - - +
5115E ARG* 3.3 5.4 + - - +
5130E ALA* 2.9 21.6 + - - +
5156E THR* 3.1 11.1 + - - -
5158E SER* 4.0 10.3 - - - -
5199E SER* 2.6 34.8 + - - -
5200E ALA* 4.1 9.4 - - - -
5203E LEU* 3.3 10.2 - - - +
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Residues in contact with VAL5114 (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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1127A GLU* 3.6 17.7 - - + +
1128A PHE* 4.1 14.6 - - + -
1129A PRO* 3.9 5.2 - - + -
5113E SER* 1.3 73.1 - - - +
5115E ARG* 1.3 58.9 + - - +
5116E LEU* 3.0 30.2 + - + -
5155E VAL* 4.5 2.7 - - + -
5156E THR 2.6 21.0 + - - +
5157E ALA* 3.9 12.1 - - + -
5158E SER* 3.0 27.2 + - - +
5187E TRP* 3.9 22.2 - - + -
5192E VAL* 3.8 27.6 - - + -
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Residues in contact with ARG5115 (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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1127A GLU* 3.0 33.0 + - - +
5113E SER 3.9 1.3 - - - +
5114E VAL* 1.3 69.9 - - - +
5116E LEU* 1.3 57.3 + - - +
5117E ASP* 3.2 18.8 + - - +
5120E SER* 3.1 37.8 + - - +
5121E LEU* 3.3 12.7 - - - +
5124E ALA 2.8 23.2 + - - -
5125E PRO 2.8 24.9 + - - -
5126E MET* 3.3 35.7 - - - +
5128E PHE* 2.9 28.8 + - - +
5129E PRO* 5.3 0.2 - - - -
5130E ALA* 3.7 23.6 - - + +
5179E ARG* 5.3 1.4 + - - -
5200E ALA* 4.1 5.4 - - + -
5204E THR* 4.0 13.0 - - - +
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Residues in contact with LEU5116 (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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1127A GLU* 4.0 13.2 - - + -
2122C HIS* 3.1 18.5 + - + +
5114E VAL* 3.0 26.1 + - + -
5115E ARG* 1.3 75.9 - - - +
5117E ASP* 1.3 56.4 + - - +
5157E ALA* 3.9 27.6 - - + -
5158E SER 3.0 19.5 + - - +
5159E SER* 3.8 8.1 - - - -
5160E ASP 3.0 19.2 + - - -
5165E GLY 4.5 9.0 - - - +
5179E ARG* 4.4 11.4 - - - +
5180E PHE* 4.1 20.4 - - + -
5187E TRP* 3.9 28.3 - - + +
5195E TYR* 4.7 0.4 - - + -
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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