Contacts of the helix formed by residues 130 - 142 (chain K) in PDB entry 3SDI
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 GLY 130 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1K THR 3.0 9.1 + - - -
2K THR* 3.1 23.7 - - - +
129K SER* 1.3 72.6 - - - +
131K GLN* 1.3 65.0 + - - +
132K THR 3.2 3.3 + - - -
133K PHE* 3.2 24.7 + - - +
134K ALA 3.3 9.0 + - - -
162K ALA* 3.5 7.2 - - - +
166K ASP* 3.1 14.3 + - - -
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Residues in contact with GLN 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J ARG* 4.6 7.1 + - - +
24J ILE* 5.2 4.6 - - + +
25J SER* 2.9 36.6 + - - +
27J LEU* 3.9 15.2 - - - +
2K THR* 4.4 4.0 - - - +
126K CYS* 3.5 34.1 + - + +
127K VAL* 3.7 5.5 - - - +
128K GLY* 2.9 31.8 + - - +
129K SER 3.2 2.2 + - - +
130K GLY* 1.3 78.7 - - - +
132K THR* 1.3 63.4 + - + +
134K ALA* 3.4 1.0 + - - +
135K TYR* 2.9 34.3 + - + -
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Residues in contact with THR 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ILE* 3.8 22.2 - - + -
25J SER* 3.6 17.0 - - - +
129K SER 4.7 3.4 + - - +
131K GLN* 1.3 74.8 - - + +
133K PHE* 1.3 66.8 + - - +
135K TYR* 3.3 5.5 + - - +
136K GLY* 2.9 24.9 + - - -
132X PHE* 2.9 42.5 + - + +
133X TYR* 3.5 39.2 - - + +
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Residues in contact with PHE 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K SER 4.3 7.2 - - - -
130K GLY* 3.2 19.4 + - - +
132K THR* 1.3 74.5 + - - +
134K ALA* 1.3 66.9 + - - +
136K GLY 2.9 8.5 + - - -
137K VAL* 3.4 6.4 + - - +
161K ALA* 4.4 1.1 - - - -
162K ALA* 3.5 20.0 - - - -
165K ARG* 3.5 30.7 - - + -
166K ASP* 3.6 28.7 - - + -
24W SER* 5.5 0.7 - - - -
25W LEU* 3.6 26.2 - - + -
131X GLY 4.2 3.6 - - - -
132X PHE* 3.3 49.1 - + - -
136X SER* 2.9 34.1 + - - +
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Residues in contact with ALA 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K THR* 3.7 26.2 - - + -
4K LEU* 4.9 5.2 - - + -
126K CYS* 3.8 17.0 - - + -
130K GLY 3.3 3.6 + - - -
131K GLN 3.6 8.1 - - - +
133K PHE* 1.3 77.2 - - - +
135K TYR* 1.3 63.7 + - - +
137K VAL 3.4 0.3 + - - -
138K LEU* 3.0 24.9 + - - +
158K SER* 3.7 28.6 + - - +
162K ALA* 3.8 3.2 - - - +
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Residues in contact with TYR 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J SER* 4.3 12.8 - - - -
26J VAL 5.0 0.2 - - - -
27J LEU* 3.7 16.1 - - + +
124K ILE* 4.3 10.5 + - + -
125K PHE* 3.7 8.9 - - - -
126K CYS* 3.2 53.5 + - + -
131K GLN* 2.9 41.4 + - + -
132K THR* 3.4 13.0 - - - +
134K ALA* 1.3 71.8 - - - +
136K GLY* 1.3 56.5 + - - +
138K LEU* 4.4 1.8 - - + -
139K ASP* 2.9 34.6 + - - +
133X TYR* 4.5 7.4 - + + -
161X GLU* 2.9 17.5 - - - +
165X ARG* 3.3 47.3 + - + -
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Residues in contact with GLY 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K THR 2.9 10.1 + - - -
133K PHE 2.9 9.4 + - - -
135K TYR* 1.3 77.0 - - - +
137K VAL* 1.3 60.3 + - - +
139K ASP* 4.4 0.2 - - - +
140K SER* 3.0 25.5 + - - -
133X TYR* 3.9 17.9 - - - -
136X SER* 4.0 1.3 - - - -
137X LEU* 3.6 11.6 - - - +
161X GLU* 3.4 16.5 + - - +
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Residues in contact with VAL 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K PHE 3.4 1.2 + - - -
134K ALA 3.4 3.4 + - - +
136K GLY* 1.3 71.9 - - - +
138K LEU* 1.3 68.9 + - - +
140K SER* 3.0 17.6 + - - -
141K ASN* 3.2 22.9 + - - +
154K LEU* 4.1 13.9 - - + -
157K ARG* 4.3 15.7 - - + +
158K SER* 3.6 18.2 - - - +
161K ALA* 3.5 28.7 - - + -
136X SER* 3.6 22.9 + - - +
137X LEU* 4.8 1.3 - - - +
140X HIS* 4.2 19.7 - - + -
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Residues in contact with LEU 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K LEU* 4.8 8.1 - - + -
6K PHE* 3.7 37.0 - - + -
124K ILE* 3.5 32.3 - - + -
125K PHE 5.2 0.4 - - - +
126K CYS* 3.9 20.0 - - - -
134K ALA 3.0 21.4 + - - +
135K TYR* 4.0 3.1 - - + +
137K VAL* 1.3 73.9 - - - +
139K ASP* 1.3 64.8 + - - +
141K ASN 3.3 0.9 + - - -
142K TYR* 3.0 33.7 + - + +
154K LEU* 3.7 29.7 - - + +
158K SER* 3.3 13.1 + - - +
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Residues in contact with ASP 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K ILE* 4.6 10.9 - - - +
135K TYR* 2.9 25.7 + - - +
138K LEU* 1.3 75.5 - - - +
140K SER* 1.3 59.3 + - - +
141K ASN 3.6 0.3 + - - -
142K TYR* 3.9 14.2 + - - +
161X GLU* 2.9 34.0 - - - +
164X LYS* 3.9 17.1 - - + +
165X ARG* 2.7 45.8 + - - +
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Residues in contact with SER 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136K GLY 3.0 20.1 + - - -
137K VAL* 3.0 7.3 + - - -
139K ASP* 1.3 78.8 - - - +
141K ASN* 1.3 62.6 + - - +
142K TYR 5.5 0.4 - - - -
137X LEU* 3.1 29.0 - - - +
141X HIS* 3.3 16.2 + - - -
157X LEU* 4.4 20.5 - - - +
161X GLU* 5.6 2.7 - - - -
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Residues in contact with ASN 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137K VAL* 3.2 11.7 + - - +
138K LEU 3.8 0.2 - - - -
140K SER* 1.3 79.3 + - - +
142K TYR* 1.3 62.3 + - - +
143K LYS* 3.6 3.1 + - - +
146K LEU* 4.2 11.6 - - - +
154K LEU* 3.6 29.8 - - + +
140X HIS* 3.3 21.1 + - - -
141X HIS* 3.1 36.7 + - - -
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Residues in contact with TYR 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K PHE* 3.8 25.8 - + - -
7K ARG 2.7 29.3 + - - -
8K PHE* 4.6 2.0 - - + -
123K ASP* 4.9 4.7 + - - +
124K ILE* 4.1 31.0 - - + +
138K LEU* 3.0 23.6 + - + +
139K ASP* 3.9 12.8 + - - +
140K SER 3.7 1.6 - - - -
141K ASN* 1.3 79.8 - - - +
143K LYS* 1.3 86.0 + - - +
144K TRP* 3.5 23.1 - - + -
146K LEU* 4.4 5.2 - - + -
154K LEU* 3.9 8.1 - - + -
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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