Contacts of the strand formed by residues 3212 - 3222 (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 ARG3212 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3087D ARG* 2.9 12.6 + - - +
3088D THR* 2.9 31.7 + - - +
3089D PHE* 2.8 27.7 + - - -
3133D ASP* 3.2 33.2 - - - +
3135D ALA* 3.4 26.2 - - - +
3136D CYS* 3.9 9.4 - - - -
3210D GLY 5.1 4.3 - - - +
3211D LEU* 1.3 72.0 - - - +
3213D ALA* 1.3 62.3 + - - +
3252D LEU* 3.6 28.7 + - - +
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Residues in contact with ALA3213 (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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3089D PHE* 3.0 10.3 - - + +
3132D ALA* 3.5 5.9 - - - +
3133D ASP* 2.9 31.3 + - - +
3136D CYS* 3.9 6.7 - - - +
3202D LEU* 4.2 11.2 - - + -
3203D LEU* 4.2 16.6 - - + -
3206D CYS* 3.8 28.0 - - + +
3211D LEU 3.9 1.0 + - - -
3212D ARG* 1.3 76.6 - - - +
3214D GLY* 1.3 59.3 + - - +
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Residues in contact with GLY3214 (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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3089D PHE 2.8 8.9 + - - +
3090D LEU* 3.8 6.3 - - - -
3091D ARG* 3.0 26.6 + - - +
3132D ALA* 4.5 6.1 - - - -
3136D CYS* 3.7 17.9 - - - +
3137D THR* 4.9 1.3 - - - -
3140D LEU* 3.8 9.4 - - - -
3202D LEU* 4.1 3.6 - - - +
3203D LEU* 4.8 2.2 - - - -
3213D ALA* 1.3 76.2 - - - +
3215D MET* 1.3 61.9 + - - +
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Residues in contact with MET3215 (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* 3.2 46.0 - - + +
3108D LEU 5.4 0.7 - - - +
3109D VAL* 3.5 3.8 - - - +
3110D THR* 2.9 65.7 + - + +
3132D ALA* 5.0 0.2 - - - +
3140D LEU* 3.4 9.7 - - - +
3156D THR* 5.3 0.7 - - + -
3194D ASN* 5.3 1.6 - - - +
3196D GLU* 3.6 32.5 - - + +
3199D SER* 4.1 10.3 - - - -
3202D LEU* 5.1 0.9 - - + -
3203D LEU* 4.6 11.4 - - + -
3214D GLY* 1.3 74.8 - - - +
3216D VAL* 1.3 63.5 + - - +
3217D ALA* 3.7 29.6 - - + -
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Residues in contact with VAL3216 (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 2.9 17.5 + - - +
3092D ILE* 3.2 15.3 - - + -
3093D GLY 3.0 19.1 + - - -
3107D VAL* 3.6 28.3 - - + -
3108D LEU 3.4 4.9 - - - +
3109D VAL* 4.4 8.1 - - + +
3140D LEU* 3.8 16.6 - - + -
3215D MET* 1.3 77.6 - - - +
3217D ALA* 1.3 66.9 + - - +
3241D ALA* 4.8 5.8 - - + +
3244D ILE* 4.3 16.4 - - + -
3245D VAL* 3.9 24.0 - - + -
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Residues in contact with ALA3217 (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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3093D GLY 3.1 16.8 - - - +
3094D THR 4.4 0.2 - - - -
3095D THR* 3.6 23.8 - - + -
3106D ASP 3.8 0.3 - - - +
3107D VAL* 3.4 4.0 - - - +
3108D LEU* 2.9 37.1 + - + +
3194D ASN* 4.8 2.2 - - - +
3215D MET* 3.7 20.9 - - + -
3216D VAL* 1.3 79.5 - - - +
3218D GLY* 1.3 60.1 + - - +
3219D VAL 4.0 0.3 + - - -
3241D ALA* 4.7 6.7 - - - -
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Residues in contact with GLY3218 (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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3093D GLY 2.9 11.1 + - - -
3094D THR* 3.4 6.1 - - - -
3095D THR* 2.9 22.9 + - - -
3106D ASP 3.5 5.8 - - - -
3107D VAL* 4.8 1.3 - - - -
3217D ALA* 1.3 73.7 - - - +
3219D VAL* 1.3 63.2 + - - -
3220D ILE* 3.4 3.1 + - - +
3237D THR* 3.4 22.4 - - - -
3238D GLU* 6.2 0.2 - - - -
3241D ALA* 4.4 11.2 - - - +
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Residues in contact with VAL3219 (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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3095D THR* 3.3 9.9 - - + +
3097D ALA* 4.1 10.5 - - + -
3102D ILE* 3.9 15.0 - - + -
3103D ASN 3.9 5.4 - - - +
3104D VAL* 3.4 23.6 - - - +
3105D GLY 2.8 28.4 + - - +
3106D ASP* 2.9 20.0 + - + +
3108D LEU* 3.7 33.0 - - + -
3218D GLY* 1.3 70.8 - - - -
3220D ILE* 1.3 60.8 + - - +
3221D VAL 3.4 22.0 - - - +
3233D THR* 5.0 0.2 + - - -
3237D THR* 3.7 9.8 + - - +
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Residues in contact with ILE3220 (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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6007B PHE* 4.3 17.7 - - + -
3094D THR* 3.8 24.5 - - + +
3095D THR 3.0 11.2 + - - +
3104D VAL* 3.4 15.3 - - - +
3218D GLY 3.8 10.8 - - - +
3219D VAL* 1.3 77.7 - - - +
3221D VAL* 1.3 67.7 + - + +
3229D PRO* 4.8 11.1 - - - +
3233D THR* 4.0 9.7 + - - -
3234D MET* 3.4 51.3 - - + +
3237D THR* 4.7 4.0 - - + -
8003D URA 3.9 28.0 - - + -
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Residues in contact with VAL3221 (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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3095D THR 3.8 0.2 + - - -
3096D GLY* 3.2 9.4 - - - -
3097D ALA 2.9 23.6 + - - -
3104D VAL* 3.5 10.4 - - + +
3168D ARG* 4.8 7.6 - - - +
3219D VAL* 3.4 5.0 - - - +
3220D ILE* 1.3 85.4 - - + +
3222D ASN* 1.3 72.5 + - - +
3223D ARG* 4.7 8.3 - - - +
3227D GLU 5.2 9.0 - - - +
3229D PRO* 6.1 4.9 - - + -
8003D URA 3.7 29.8 - - + +
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Residues in contact with ASN3222 (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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3097D ALA* 3.5 8.1 - - - +
3099D GLN 3.1 18.0 + - - -
3100D PRO 4.2 0.8 + - - -
3102D ILE 2.5 29.8 + - - +
3103D ASN* 5.0 0.2 - - - -
3104D VAL* 3.9 9.3 - - + +
3221D VAL* 1.3 82.3 - - - +
3223D ARG* 1.3 55.1 + - - +
3224D THR* 2.6 57.6 + - - +
3225D GLN* 3.1 51.9 + - + +
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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