Contacts of the helix formed by residues 145 - 157 (chain H) in PDB entry 1YI2
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 ASP 145 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H LEU* 5.6 0.2 - - - +
80H LEU* 3.1 47.6 - - + +
85H ASP* 4.4 8.0 + - - +
141H CYS* 4.0 10.8 - - + -
142H ASN* 2.8 30.9 + - - +
144H GLU* 1.3 79.3 - - - +
146H ALA* 1.3 63.8 + - - +
147H GLU 3.3 2.5 - - - -
148H HIS* 2.9 23.6 + - - +
149H VAL* 3.2 12.0 + - - +
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Residues in contact with ALA 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H VAL* 4.5 18.8 - - + -
50H ILE* 4.5 5.2 - - + -
141H CYS* 3.8 3.6 - - - -
142H ASN 3.5 3.2 + - - -
143H VAL* 3.6 17.9 - - + +
144H GLU 3.2 3.0 - - - -
145H ASP* 1.3 75.7 - - - +
147H GLU* 1.3 65.8 + - + +
149H VAL* 2.8 31.0 - - - +
150H LYS* 3.0 18.6 + - - +
174H LEU* 6.5 1.1 - - + -
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Residues in contact with GLU 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144H GLU 4.4 5.4 + - - +
145H ASP 3.3 1.0 - - - -
146H ALA* 1.3 79.7 - - + +
148H HIS* 1.3 64.1 + - + +
150H LYS* 3.4 40.8 + - - +
151H GLU* 3.3 21.1 + - - +
174H LEU* 5.5 3.8 - - - +
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Residues in contact with HIS 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H HIS* 3.7 10.2 + - - -
76H LEU* 4.0 10.3 - - + +
79H GLU* 2.9 48.5 + - + +
80H LEU* 3.8 26.8 - - + +
144H GLU 4.6 4.5 + - - -
145H ASP* 2.9 24.8 + - - +
147H GLU* 1.3 80.8 - - + +
149H VAL* 1.3 60.4 + - - +
151H GLU* 3.0 7.4 + - - +
152H ALA* 2.9 24.9 + - - +
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Residues in contact with VAL 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE* 3.4 26.2 - - + -
76H LEU* 3.9 18.8 - - + +
139H ALA* 3.4 34.8 - - + -
141H CYS* 3.7 15.5 - - + -
145H ASP 3.2 3.0 + - - +
146H ALA* 2.8 33.0 - - - +
148H HIS* 1.3 79.5 - - - +
150H LYS* 1.3 61.5 + - - +
152H ALA* 3.3 2.2 + - + +
153H PHE* 3.2 37.7 + - + -
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Residues in contact with LYS 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE* 4.0 13.7 - - + -
146H ALA* 3.0 20.7 + - - +
147H GLU* 3.4 38.9 + - - +
148H HIS 3.2 0.2 - - - -
149H VAL* 1.3 78.7 - - - +
151H GLU* 1.3 61.9 + - - +
153H PHE 4.0 0.2 - - - -
154H ARG* 3.2 18.4 + - - +
166H ILE* 3.3 33.7 - - + +
168H VAL* 3.7 27.7 - - - +
174H LEU* 4.9 15.7 - - - +
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Residues in contact with GLU 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H HIS* 3.5 25.1 - - + +
147H GLU 3.3 13.6 + - - +
148H HIS* 3.0 10.5 + - - +
150H LYS* 1.3 81.3 - - - +
152H ALA* 1.3 64.6 + - - +
153H PHE 3.2 0.2 - - - -
154H ARG* 3.1 54.5 + - - +
155H ARG* 3.3 23.2 + - - +
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Residues in contact with ALA 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H ALA* 3.4 41.5 - - + +
75H HIS* 3.9 11.6 - - + -
76H LEU* 4.0 17.0 - - + -
148H HIS 2.9 11.9 + - - +
149H VAL* 3.6 8.7 - - - +
151H GLU* 1.3 75.8 - - - +
153H PHE* 1.3 63.6 + - + +
155H ARG* 3.2 6.8 + - - +
156H ALA 3.0 21.3 + - - -
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Residues in contact with PHE 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H ILE* 3.1 44.0 - - + -
51H SER 3.7 13.0 - - - -
52H LEU* 3.7 22.4 - - + +
72H ALA* 4.9 3.8 - - + -
88H MET* 3.6 26.7 - - - -
137H PHE* 3.9 21.1 - + + -
138H THR 4.4 0.2 - - - -
139H ALA* 3.8 18.4 - - + -
149H VAL* 3.2 19.2 + - + +
151H GLU 3.2 0.2 - - - -
152H ALA* 1.3 78.3 - - + +
154H ARG* 1.3 65.1 + - - +
155H ARG 3.0 2.0 - - - -
156H ALA* 3.7 6.9 - - + +
157H TYR* 2.9 28.4 + - - +
166H ILE* 3.6 25.1 - - + -
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Residues in contact with ARG 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11350 G 4.3 8.1 - - - +
25020 C 3.1 15.4 + - - -
25030 A 2.4 31.9 + - - -
150H LYS 3.2 12.1 + - - +
151H GLU* 3.1 39.6 + - - +
153H PHE* 1.3 78.3 - - - +
155H ARG* 1.3 72.2 + - - +
157H TYR* 3.1 41.8 - - + +
158H ASN* 2.9 29.1 + - - +
166H ILE* 3.8 3.8 - - + +
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Residues in contact with ARG 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25020 C 4.3 13.1 + - - +
25030 A 3.8 28.3 + - - -
25040 A 2.8 34.9 + - - -
71H SER* 3.8 31.1 + - - +
75H HIS* 4.0 35.4 + - - +
151H GLU* 3.4 20.3 + - - +
152H ALA 3.2 6.7 + - - +
153H PHE 3.0 0.6 - - - -
154H ARG* 1.3 96.7 - - - +
156H ALA* 1.3 64.7 + - - +
158H ASN* 3.3 17.2 + - - +
159H LYS* 3.9 7.6 + - - +
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Residues in contact with ALA 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H LEU* 4.4 6.1 - - + -
68H SER* 3.2 47.0 - - - +
71H SER* 4.0 1.3 + - - -
72H ALA* 3.9 8.3 - - + -
137H PHE* 4.4 13.2 - - + -
152H ALA 3.0 15.9 + - - +
153H PHE* 3.1 9.6 + - + +
155H ARG* 1.3 73.4 - - - +
157H TYR* 1.3 56.5 + - - +
158H ASN 3.1 8.1 + - - -
159H LYS* 3.2 11.8 + - - -
160H ILE* 3.9 5.3 - - - +
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Residues in contact with TYR 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11340 G 3.9 16.1 + - - +
11350 G 2.8 36.2 + - - -
52H LEU* 4.1 16.8 - - + +
153H PHE 2.9 18.7 + - - +
154H ARG* 3.1 35.9 - - + +
156H ALA* 1.3 75.4 - - - +
158H ASN* 1.3 72.7 + - - +
159H LYS 3.2 2.4 + - - -
160H ILE* 3.7 14.1 - - - +
164H CYS* 3.7 37.5 - - + -
166H ILE* 4.1 13.9 - - + -
8509H NA 2.9 24.8 - - - -
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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