Contacts of the helix formed by residues 3198 - 3208 (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 GLU3198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3026D GLY* 5.7 0.2 - - - -
3067D THR* 4.5 3.1 - - - +
3068D GLY 4.3 7.9 - - - +
3069D ILE* 3.5 9.9 - - - +
3070D GLY 2.6 33.2 + - - +
3071D GLY* 4.7 2.7 - - - +
3074D THR* 3.1 30.5 - - + +
3091D ARG* 2.7 48.7 + - - +
3158D SER* 3.7 0.7 - - - -
3196D GLU* 2.8 8.5 + - - +
3197D MET* 1.3 89.2 + - - +
3199D SER* 1.3 58.0 + - - +
3200D ALA 3.4 2.7 - - - -
3201D THR* 3.3 6.5 + - - +
3202D LEU* 2.9 28.7 + - - +
7003D SO4 4.2 6.8 + - - -
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Residues in contact with SER3199 (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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3091D ARG* 4.2 4.2 - - - +
3110D THR* 4.7 0.9 - - - -
3113D SER* 3.0 24.4 + - - -
3156D THR* 3.8 3.0 - - - +
3158D SER* 3.3 5.4 - - - -
3196D GLU* 2.3 44.8 + - - +
3198D GLU* 1.3 71.2 - - - +
3200D ALA* 1.3 55.4 + - - +
3202D LEU* 4.3 6.5 - - - -
3203D LEU* 2.7 40.7 + - - +
3215D MET* 4.1 23.3 - - - -
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Residues in contact with ALA3200 (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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3113D SER* 4.0 8.7 - - - -
3114D VAL 4.3 0.7 - - - +
3115D ARG* 3.9 20.4 - - + -
3117D ASP* 3.3 26.7 - - - +
3120D SER* 3.7 1.4 - - - -
3130D ALA* 3.9 4.9 - - - +
3158D SER* 3.1 26.1 + - - +
3199D SER* 1.3 76.8 + - - +
3201D THR* 1.3 57.8 + - - +
3204D THR* 2.6 35.9 + - - -
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Residues in contact with THR3201 (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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3071D GLY* 3.3 43.6 - - - +
3074D THR* 4.9 2.2 - - + -
3075D SER* 4.2 12.6 - - - +
3117D ASP* 2.6 26.1 + - - +
3119D ALA* 3.5 20.3 - - + +
3120D SER* 4.3 4.9 - - - +
3123D PHE* 4.5 3.5 - - + -
3198D GLU* 3.3 6.2 + - - -
3200D ALA* 1.3 75.0 - - - +
3202D LEU* 1.3 67.6 + - - +
3205D MET* 3.0 34.5 + - - +
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Residues in contact with LEU3202 (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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3024D VAL* 4.7 6.5 - - + -
3074D THR* 4.4 11.6 - - + +
3078D VAL* 4.0 24.5 - - + -
3089D PHE* 4.2 14.6 - - + +
3091D ARG* 3.4 40.2 - - + +
3198D GLU 2.9 18.0 + - - +
3199D SER* 3.8 3.8 - - - +
3201D THR* 1.3 80.7 - - - +
3203D LEU* 1.3 70.6 + - + +
3205D MET* 3.5 5.4 - - - +
3206D CYS* 3.2 37.1 + - - +
3213D ALA* 4.2 7.6 - - + -
3214D GLY 4.1 12.1 - - - +
3215D MET* 5.1 1.1 - - + -
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Residues in contact with LEU3203 (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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3110D THR* 3.7 18.6 - - + -
3113D SER* 3.6 17.5 - - - +
3130D ALA* 3.5 32.5 - - - +
3131D VAL 3.9 5.2 + - - +
3132D ALA* 3.9 29.8 - - + +
3199D SER* 2.7 30.6 + - - +
3202D LEU* 1.3 80.7 - - + +
3204D THR* 1.3 57.0 + - - +
3206D CYS* 4.0 3.0 - - - +
3207D ALA* 3.0 31.7 + - - +
3213D ALA* 4.1 20.6 - - + +
3215D MET* 4.6 8.7 - - + -
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Residues in contact with THR3204 (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* 3.8 19.8 + - - +
3120D SER* 3.6 34.0 - - - +
3123D PHE* 4.6 1.1 - - + -
3124D ALA* 4.0 15.9 - - + +
3128D PHE* 4.4 5.6 - - + -
3129D PRO 5.1 1.1 - - - -
3130D ALA* 3.2 21.7 - - - +
3200D ALA 2.6 25.0 + - - -
3201D THR 4.3 0.2 - - - -
3203D LEU* 1.3 72.6 - - - +
3205D MET* 1.3 65.7 + - - +
3206D CYS 3.1 1.8 - - - -
3207D ALA* 3.3 3.5 + - - +
3208D SER* 2.9 31.1 + - - +
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Residues in contact with MET3205 (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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3075D SER* 3.8 32.5 - - - +
3078D VAL* 3.7 37.5 - - + -
3079D GLU* 4.3 9.2 - - + +
3123D PHE* 3.4 55.6 - - + +
3201D THR* 3.0 28.0 + - - +
3202D LEU* 3.5 7.0 - - - +
3204D THR* 1.3 79.7 - - - +
3206D CYS* 1.3 63.3 + - - +
3208D SER* 3.7 0.7 + - - -
3209D GLN* 3.2 43.0 + - - +
3211D LEU* 4.8 0.6 - - + +
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Residues in contact with CYS3206 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3078D VAL* 4.2 8.3 - - - -
3089D PHE* 4.0 15.3 - - - -
3202D LEU* 3.2 25.3 + - - +
3203D LEU 4.1 1.8 - - - +
3204D THR 3.1 1.0 - - - -
3205D MET* 1.3 78.9 - - - +
3207D ALA* 1.3 61.8 + - - +
3208D SER 3.1 5.8 + - - -
3209D GLN 3.3 0.2 + - - -
3210D GLY* 3.3 4.9 + - - -
3211D LEU* 2.8 65.7 + - - +
3213D ALA* 3.8 24.7 - - + -
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Residues in contact with ALA3207 (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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2155C VAL* 5.1 4.8 - - + +
2190C MET 2.9 17.7 - - - +
2191C GLY* 5.1 0.2 - - - -
3128D PHE* 3.7 23.3 - - + -
3129D PRO 4.8 0.9 - - - +
3131D VAL* 3.9 23.6 - - + +
3203D LEU 3.0 19.7 + - - +
3204D THR 4.2 0.2 - - - +
3206D CYS* 1.3 75.8 - - - +
3208D SER* 1.3 58.6 + - - +
3209D GLN 3.5 0.4 - - - -
3210D GLY* 4.6 2.3 + - - -
3211D LEU 4.4 2.7 - - - -
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Residues in contact with SER3208 (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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6175B ARG* 2.9 36.1 + - - -
2189C ALA 3.6 4.5 - - - +
2190C MET* 3.4 27.4 - - - +
3123D PHE* 4.3 7.2 - - - -
3124D ALA* 3.5 21.1 - - - +
3128D PHE* 3.7 12.1 - - - -
3204D THR 2.9 21.6 + - - -
3205D MET* 4.1 5.2 - - - -
3207D ALA* 1.3 78.8 - - - +
3209D GLN* 1.3 58.6 + - - +
3210D GLY 3.8 0.7 - - - -
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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