Contacts of the helix formed by residues 3118 - 3123 (chain D) 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 GLY3118 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6117B ASP 4.4 3.8 - - - -
6118B GLY* 3.9 9.9 - - - -
6160B ASP* 3.5 14.1 - - - -
6179B ARG* 4.8 0.3 + - - -
3117D ASP* 1.3 76.3 - - - +
3119D ALA* 1.3 67.1 + - - +
3120D SER 3.2 2.2 - - - -
3121D LEU* 3.1 25.6 + - - +
3122D HIS* 3.2 17.4 - - - -
3160D ASP* 3.0 8.1 + - - -
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Residues in contact with ALA3119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6160B ASP* 3.6 32.3 + - + +
6161B THR* 3.8 8.1 - - + -
3071D GLY* 4.0 10.8 - - - -
3072D PRO* 4.3 1.1 - - + +
3117D ASP* 3.6 1.2 + - + +
3118D GLY* 1.3 73.9 - - - +
3120D SER* 1.3 61.0 + - - +
3122D HIS* 2.8 23.6 + - - +
3123D PHE* 3.0 16.9 - - - -
3160D ASP* 4.8 0.4 + - - -
3201D THR* 3.5 28.5 - - + +
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Residues in contact with SER3120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3115D ARG* 2.8 38.8 + - - +
3117D ASP* 2.9 30.4 + - - -
3118D GLY 4.7 0.3 + - - -
3119D ALA* 1.3 76.8 - - - +
3121D LEU* 1.3 62.3 + - - +
3123D PHE* 3.0 12.1 + - - +
3124D ALA 3.0 25.5 + - - +
3126D MET* 5.3 0.7 - - - +
3200D ALA 3.7 7.6 - - - -
3201D THR* 3.9 3.3 + - - +
3204D THR* 3.6 21.9 - - - +
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Residues in contact with LEU3121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6117B ASP 6.1 0.4 - - - +
6121B LEU* 6.4 1.8 - - + -
6177B VAL* 3.8 12.3 - - - +
6179B ARG* 3.6 29.7 - - - +
6180B PHE* 4.1 5.4 - - - -
3115D ARG* 3.9 2.9 - - - +
3117D ASP 4.5 3.4 - - - +
3118D GLY* 3.1 22.8 + - - +
3119D ALA 3.1 0.6 - - - -
3120D SER* 1.3 78.3 + - - +
3122D HIS* 1.3 59.0 + - - +
3123D PHE 3.1 6.2 + - - -
3124D ALA 3.4 10.5 + - - +
3125D PRO* 4.2 3.6 - - + +
3126D MET* 3.5 59.2 - - + +
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Residues in contact with HIS3122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6116B LEU* 3.1 29.4 + - + -
6117B ASP* 5.0 0.4 - - - -
6159B SER* 3.3 18.8 - - - -
6160B ASP* 3.3 10.1 + - - +
6161B THR* 2.6 35.1 + - + +
6164B PRO* 3.3 26.1 - - + +
6165B GLY* 3.2 8.2 - - - +
6175B ARG* 5.6 0.2 + - - -
6177B VAL* 3.3 14.4 + - - +
6179B ARG* 4.3 6.0 + - - -
6180B PHE* 3.6 32.7 - + + -
3118D GLY 3.2 21.5 + - - -
3119D ALA* 2.8 10.8 + - - +
3121D LEU* 1.3 78.8 - - - +
3123D PHE* 1.3 59.6 + - + +
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Residues in contact with PHE3123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6161B THR* 3.9 13.7 - - + -
6164B PRO* 3.8 27.1 - - + -
6175B ARG* 3.5 18.1 + - - +
6177B VAL* 3.7 6.0 - - - +
2190C MET* 3.2 19.1 - - - +
3075D SER* 4.1 14.4 - - - -
3079D GLU* 5.7 2.7 - - + -
3119D ALA 3.0 31.2 - - - -
3120D SER* 3.0 8.4 + - - +
3122D HIS* 1.3 83.7 - - + +
3124D ALA* 1.3 59.8 + - - +
3201D THR* 4.5 2.2 - - + -
3204D THR* 4.6 2.7 - - + -
3205D MET* 3.4 64.8 - - + +
3208D SER* 4.7 4.3 - - - -
3209D GLN* 4.0 22.9 - - - -
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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