Contacts of the helix formed by residues 121 - 135 (chain K) in PDB entry 1P7G
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 SER 121 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115K ILE* 4.1 3.1 - - - -
116K ASN* 3.1 15.2 + - - +
119K PHE* 3.1 5.1 - - - +
120K GLY* 1.3 80.8 - - - +
122K PHE* 1.3 61.3 + - - +
123K GLU* 2.8 26.2 + - - +
124K LYS* 3.3 19.6 + - - +
125K PHE* 3.0 21.8 + - - +
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Residues in contact with PHE 122 (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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105K GLY 4.1 10.1 - - - -
106K LYS* 4.1 30.3 - - + -
107K PRO* 3.4 25.6 - - + -
115K ILE* 3.9 10.8 - - + -
116K ASN* 3.5 7.7 + - - +
121K SER* 1.3 71.2 - - - +
123K GLU* 1.3 71.9 + - + +
125K PHE* 3.1 20.6 + + - +
126K LYS* 2.7 54.4 + - + +
198K TRP* 4.1 17.9 - + + -
203K TRP* 3.4 32.1 - + - -
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Residues in contact with GLU 123 (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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106K LYS* 4.6 14.1 + - - +
121K SER* 2.8 32.6 + - - +
122K PHE* 1.3 92.3 + - + +
124K LYS* 1.3 56.9 + - - +
126K LYS* 3.2 9.2 + - - +
127K GLU* 2.9 27.1 + - - +
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Residues in contact with LYS 124 (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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64J PHE* 2.8 42.6 + - + -
65J ARG* 3.4 30.1 - - + +
66J LYS 5.4 0.4 - - - -
67J GLY* 4.8 6.3 - - - +
119K PHE* 3.4 28.3 - - + +
121K SER* 3.3 13.3 + - - +
123K GLU* 1.3 74.7 - - - +
125K PHE* 1.3 66.5 + - - +
127K GLU* 2.8 33.0 + - - +
128K GLU* 2.8 21.9 + - - +
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Residues in contact with PHE 125 (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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115K ILE* 3.6 21.8 - - + -
119K PHE* 3.7 34.5 - + + +
121K SER 3.0 14.7 + - - +
122K PHE* 3.4 23.6 - + - +
124K LYS* 1.3 76.6 - - - +
126K LYS* 1.3 59.1 + - - +
128K GLU* 3.6 0.7 - - - +
129K PHE* 2.8 48.3 + + + +
144K LEU* 3.9 33.2 - - + -
155K ILE* 3.6 21.3 - - + -
173K LEU* 4.4 3.1 - - + -
198K TRP* 3.6 20.2 - + - -
203K TRP* 3.7 21.5 - + - -
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Residues in contact with LYS 126 (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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122K PHE* 2.7 36.9 + - + +
123K GLU* 3.3 13.0 - - - +
125K PHE* 1.3 70.9 - - - +
127K GLU* 1.3 58.7 + - - +
130K SER* 2.6 40.4 + - - +
195K ASP* 5.1 4.7 + - - +
198K TRP* 3.5 62.1 - - + +
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Residues in contact with GLU 127 (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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64J PHE* 3.4 30.1 - - + -
70J GLN* 4.9 3.6 - - - +
123K GLU 2.9 13.5 + - - +
124K LYS* 2.8 36.1 + - - +
126K LYS* 1.3 76.6 - - - +
128K GLU* 1.3 57.7 + - - +
130K SER* 3.9 3.5 - - - -
131K GLN* 2.9 43.4 + - + +
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Residues in contact with GLU 128 (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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61J LEU* 3.7 16.3 - - - +
64J PHE* 4.3 17.2 - - + -
65J ARG* 2.8 52.9 + - - +
73J ILE* 4.1 18.1 - - + +
77J LEU* 5.1 0.2 - - - +
119K PHE* 3.4 15.9 - - - -
124K LYS* 2.8 19.5 + - + +
125K PHE* 3.6 5.6 - - - +
127K GLU* 1.3 75.2 - - - +
129K PHE* 1.3 63.5 + - - +
131K GLN* 3.7 3.3 - - - +
132K ALA* 3.0 22.7 + - - +
155K ILE* 3.8 21.4 + - + +
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Residues in contact with PHE 129 (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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125K PHE* 2.8 39.6 + + + +
128K GLU* 1.3 72.1 - - - +
130K SER* 1.3 64.1 + - - +
132K ALA* 3.3 4.2 + - - +
133K ALA* 3.1 18.9 + - - +
142K ALA* 3.6 22.6 - - + +
143K ILE 4.0 3.8 - - - -
144K LEU* 3.9 26.0 - - + -
155K ILE* 3.5 24.4 - - + +
173K LEU* 4.0 13.0 - - + -
175K LEU* 3.8 19.5 - - + -
194K VAL* 5.7 0.2 - - + -
197K TRP* 3.3 35.7 - + - -
198K TRP* 3.7 26.5 - + + -
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Residues in contact with SER 130 (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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126K LYS* 2.6 31.2 + - - +
127K GLU* 3.9 4.0 - - - -
129K PHE* 1.3 72.8 - - - +
131K GLN* 1.3 66.4 + - - +
133K ALA* 3.0 2.9 + - - +
134K LYS* 2.9 40.5 + - - +
194K VAL* 3.9 19.1 - - - -
195K ASP* 4.7 4.0 + - - -
198K TRP* 3.1 25.1 + - - -
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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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64J PHE* 5.3 6.1 - - + -
71J ILE* 5.4 4.2 - - + +
73J ILE* 3.4 17.0 - - + +
127K GLU* 2.9 37.6 + - + +
128K GLU* 3.7 4.9 - - - +
130K SER* 1.3 76.6 - - - +
132K ALA* 1.3 62.7 + - - +
134K LYS* 4.4 15.7 - - - +
135K ASN* 2.6 49.6 + - - +
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Residues in contact with ALA 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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73J ILE* 3.8 11.8 - - + +
77J LEU* 3.8 28.3 - - + -
128K GLU 3.0 17.2 + - - +
129K PHE 3.6 4.9 - - - +
131K GLN* 1.3 75.8 - - - +
133K ALA* 1.3 61.8 + - - +
136K VAL* 3.3 12.1 + - - +
142K ALA* 4.2 6.5 - - + -
155K ILE* 3.9 11.9 - - + -
156K LEU 4.9 0.4 - - - +
157K GLN* 2.9 28.2 - - + +
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Residues in contact with ALA 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 PHE 3.1 8.5 + - - +
130K SER 3.0 7.9 + - - +
132K ALA* 1.3 75.0 - - - +
134K LYS* 1.3 63.8 + - - +
135K ASN 3.4 0.3 + - - -
136K VAL* 3.5 8.4 + - - +
142K ALA* 3.4 24.2 - - + +
175K LEU* 3.8 17.9 - - + -
177K VAL* 3.3 41.0 - - + +
190K ARG* 3.5 1.0 - - - -
194K VAL* 4.0 8.3 - - + -
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Residues in contact with LYS 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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130K SER* 2.9 25.8 + - - +
131K GLN* 4.4 15.6 - - - +
133K ALA* 1.3 76.3 - - - +
135K ASN* 1.3 71.2 + - - +
136K VAL 3.5 0.2 - - - -
190K ARG* 3.3 25.0 + - - +
191K GLY* 3.5 27.2 + - - +
194K VAL* 3.8 21.5 - - + -
195K ASP* 3.0 37.4 + - - -
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Residues in contact with ASN 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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73J ILE* 3.9 16.0 - - + +
74J ARG* 2.9 36.8 + - + +
131K GLN* 2.6 51.3 + - - +
132K ALA 3.4 0.2 + - - -
133K ALA 3.2 0.4 - - - -
134K LYS* 1.3 85.9 - - - +
136K VAL* 1.3 63.9 + - - +
137K GLU 3.2 1.2 + - - -
157K GLN* 3.0 11.8 - - - +
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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