Contacts of the helix formed by residues 3182 - 3190 (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 GLY3182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3167D GLU* 3.1 19.0 + - - -
3181D LYS* 1.3 74.7 - - - +
3183D SER* 1.3 61.9 + - - +
3184D MET 3.3 4.4 + - - -
3185D GLU* 3.3 18.0 + - - +
3186D GLU* 3.3 15.2 + - - +
5178E ARG* 4.1 2.9 - - - -
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Residues in contact with SER3183 (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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3165D GLY 4.8 0.5 + - - -
3167D GLU* 3.9 3.8 + - - +
3179D ARG 4.2 2.9 - - - -
3180D PHE* 2.5 46.3 + - - +
3181D LYS 3.1 3.6 + - - -
3182D GLY* 1.3 76.0 - - - +
3184D MET* 1.3 61.9 + - - +
3186D GLU* 3.1 10.5 + - - +
3187D TRP* 2.9 53.8 + - - -
3195D TYR* 4.2 4.5 + - - -
5178E ARG* 3.7 9.8 - - - +
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Residues in contact with MET3184 (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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3098D ILE* 3.3 27.1 - - + -
3166D GLN 4.3 3.4 - - - +
3167D GLU* 3.0 20.1 + - + +
3183D SER* 1.3 78.8 + - - +
3185D GLU* 1.3 60.8 + - - +
3187D TRP* 3.3 3.3 + - + +
3188D GLN* 2.9 61.1 + - - +
3195D TYR* 3.3 30.1 - - + +
3223D ARG* 3.5 48.5 - - + +
3224D THR* 5.1 0.2 - - + -
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Residues in contact with GLU3185 (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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3167D GLU* 4.4 0.4 + - - -
3182D GLY* 3.3 13.2 + - - +
3184D MET* 1.3 78.2 - - - +
3186D GLU* 1.3 57.3 + - + +
3188D GLN* 3.3 17.7 + - - +
3189D ALA* 2.9 30.8 + - + +
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Residues in contact with GLU3186 (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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2125C PRO* 5.6 2.1 - - - +
3182D GLY 3.5 12.1 - - - +
3183D SER* 3.1 11.9 + - - +
3185D GLU* 1.3 74.8 - - + +
3187D TRP* 1.3 74.7 + - + +
3188D GLN 3.1 0.9 - - - -
3189D ALA* 3.1 6.4 + - - +
3190D MET* 2.9 50.3 + - + +
5177E VAL* 5.1 0.7 - - - +
5178E ARG* 2.7 63.3 + - - +
5181E LYS* 4.8 10.8 + - - +
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Residues in contact with TRP3187 (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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2125C PRO* 3.9 28.5 - - + -
2127C GLU* 4.4 3.4 - - - -
2128C PHE* 4.6 3.8 - + - -
3098D ILE* 4.3 5.4 - - + -
3114D VAL* 3.7 24.2 - - + -
3116D LEU* 3.8 38.6 - - + +
3157D ALA* 4.6 3.1 - - + -
3165D GLY 5.2 0.6 + - - -
3180D PHE* 5.2 1.7 - + - -
3183D SER* 2.9 40.4 + - - +
3184D MET* 3.3 3.6 + - - +
3186D GLU* 1.3 81.6 - - + +
3188D GLN* 1.3 60.3 + - - +
3190D MET* 3.2 20.3 + - + -
3191D GLY 3.1 4.2 + - - -
3192D VAL* 2.8 58.3 + - + +
3195D TYR* 3.1 35.3 + + + -
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Residues in contact with GLN3188 (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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3098D ILE* 2.7 39.0 + - + +
3099D GLN* 3.2 22.3 + - - +
3100D PRO* 5.2 2.6 - - - +
3184D MET* 2.9 41.7 + - - +
3185D GLU* 3.3 26.0 + - + +
3187D TRP* 1.3 77.3 - - - +
3189D ALA* 1.3 55.7 + - - +
3191D GLY* 2.7 21.8 + - - -
3224D THR* 3.8 14.5 - - - +
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Residues in contact with ALA3189 (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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2208C SER 4.0 5.5 - - - +
2209C GLN* 5.4 1.9 - - - -
3185D GLU* 2.9 19.8 + - + +
3186D GLU* 3.1 8.3 + - - +
3188D GLN* 1.3 75.3 - - - +
3190D MET* 1.3 59.7 + - - +
3191D GLY 3.2 0.7 + - - -
5175E ARG* 4.1 26.0 + - + -
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Residues in contact with MET3190 (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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2123C PHE 3.9 15.9 - - - +
2124C ALA* 4.1 7.4 - - - -
2125C PRO* 4.0 10.8 - - + -
2128C PHE* 4.1 34.8 - - + -
2207C ALA 3.5 20.8 - - - +
2208C SER* 3.4 16.2 - - - +
2210C GLY 5.4 1.5 + - - -
3186D GLU* 2.9 37.2 + - + +
3187D TRP* 3.7 18.8 - - + +
3188D GLN 3.0 0.4 - - - -
3189D ALA* 1.3 76.0 - - - +
3191D GLY* 1.3 61.0 + - - +
3192D VAL 3.3 0.9 + - - -
5175E ARG* 3.4 32.5 - - - +
5177E VAL* 4.0 12.8 - - + -
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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
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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