Contacts of the helix formed by residues 121 - 139 (chain G) in PDB entry 4PKI
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92G GLY 4.3 0.2 + - - -
119G GLU 3.7 3.1 + - - -
120G CYS* 1.3 74.4 - - - +
122G GLN* 1.3 57.4 + - - +
123G ASP* 2.8 20.7 + - - -
124G GLU* 2.7 44.5 + - - +
125G SER* 3.2 11.4 + - - -
174G SER* 3.5 20.3 + - - -
176G PHE* 5.5 1.6 - - - -
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Residues in contact with GLN 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP 5.5 0.2 - - - +
144A ALA* 2.8 39.1 + - - +
145A SER* 5.1 0.2 - - - +
334A GLU* 3.0 33.2 + - - +
341A ILE* 3.8 25.1 - - + +
345A ILE* 3.7 10.6 - - + +
120G CYS 4.0 0.6 + - - -
121G SER* 1.3 72.5 - - - +
123G ASP* 1.3 58.5 + - - +
125G SER* 3.3 8.3 + - - +
126G GLY* 2.9 27.4 + - - -
176G PHE* 4.2 11.0 - - + -
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Residues in contact with ASP 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 4.0 13.1 - - - +
73G VAL* 4.6 0.7 - - - +
75G LYS* 5.4 1.7 - - - -
76G PHE* 3.6 27.9 + - + -
121G SER* 2.8 21.6 + - - -
122G GLN* 1.3 75.6 - - - +
124G GLU* 1.3 64.4 + - - +
127G ALA* 3.0 30.7 + - - +
174G SER* 2.9 18.8 + - - -
175G GLY* 2.7 28.4 + - - -
176G PHE* 3.6 21.0 - - + -
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Residues in contact with GLU 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G VAL* 3.8 25.0 - - + +
75G LYS 5.6 3.0 + - - +
92G GLY 3.0 20.1 - - - +
93G ASP* 3.0 25.2 - - - +
94G ALA* 3.5 16.1 - - + +
120G CYS* 3.4 2.7 - - + +
121G SER* 2.7 41.7 + - - +
123G ASP* 1.3 80.3 - - - +
125G SER* 1.3 60.1 + - - +
128G ALA* 2.9 29.8 + - - +
172G VAL* 3.2 23.3 - - - +
173G ALA 4.3 3.3 - - - +
174G SER* 5.0 1.8 - - - -
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Residues in contact with SER 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA 4.9 1.6 + - - -
145A SER 5.3 0.3 - - - -
146A GLY* 3.7 15.8 + - - -
94G ALA* 4.1 0.6 - - - +
114G TYR* 5.2 0.2 - - - -
116G LEU* 3.5 37.5 - - - +
120G CYS* 4.0 12.3 + - - -
121G SER 3.2 6.9 + - - -
122G GLN* 3.3 15.2 + - - +
124G GLU* 1.3 75.4 - - - +
126G GLY* 1.3 65.8 + - - +
128G ALA* 3.4 1.9 + - - +
129G ALA* 3.1 23.7 + - - +
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Residues in contact with GLY 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR 3.2 24.7 - - - -
144A ALA* 5.0 0.4 - - - -
146A GLY* 4.4 0.4 - - - +
345A ILE* 4.1 14.6 - - - -
122G GLN 2.9 17.2 + - - -
123G ASP 4.2 0.2 - - - -
125G SER* 1.3 77.7 + - - +
127G ALA* 1.3 62.6 + - - +
129G ALA* 3.3 2.6 + - - +
130G ILE* 3.0 28.6 + - - +
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Residues in contact with ALA 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A ILE* 3.8 4.3 - - + +
349A LEU* 3.6 29.4 - - + -
73G VAL* 3.9 19.7 - - + -
76G PHE* 4.9 4.0 - - + -
123G ASP 3.0 21.4 + - - +
126G GLY* 1.3 74.1 - - - +
128G ALA* 1.3 56.6 + - - +
130G ILE* 3.2 2.3 + - - +
131G PHE* 2.8 45.9 + - + -
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Residues in contact with ALA 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G VAL* 3.8 17.4 - - + +
94G ALA* 4.0 13.0 - - + -
95G TYR 4.3 6.3 - - - +
96G VAL* 3.9 8.1 - - + +
114G TYR* 4.1 18.4 - - + -
116G LEU* 4.3 5.2 - - + -
124G GLU 2.9 18.9 + - - +
125G SER 3.7 5.4 - - - +
127G ALA* 1.3 75.7 - - - +
129G ALA* 1.3 58.0 + - - +
132G THR* 2.9 33.8 + - - -
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Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A TYR* 4.6 4.5 - - + +
146A GLY* 3.9 4.0 - - - +
147A ARG 3.9 28.3 - - - +
148A THR* 3.3 27.1 - - + +
114G TYR* 4.3 9.1 - - + -
125G SER 3.1 17.4 + - - +
126G GLY* 3.5 6.1 - - - +
128G ALA* 1.3 76.1 - - - +
130G ILE* 1.3 63.2 + - + +
132G THR* 3.3 3.1 + - - -
133G VAL* 3.1 19.2 + - - +
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Residues in contact with ILE 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A TYR* 3.6 44.2 - - + -
342A GLY 4.8 1.3 - - - +
345A ILE* 4.2 8.1 - - + -
346A LEU* 3.9 42.8 - - + +
349A LEU* 3.3 26.9 - - + -
126G GLY 3.0 17.5 + - - +
127G ALA 3.8 0.2 - - - +
129G ALA* 1.3 75.6 - - - +
131G PHE* 1.3 57.2 + - - +
133G VAL* 3.0 9.9 + - + +
134G GLN* 2.9 38.6 + - + +
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Residues in contact with PHE 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A LEU* 4.0 11.9 - - + -
350A SER* 4.0 5.6 - - - -
351A THR* 3.7 27.8 - - + -
56G HIS* 5.6 0.4 - + - -
59G PHE* 4.3 4.5 - + - -
73G VAL* 4.4 5.8 - - + -
76G PHE 3.5 24.0 - - - -
77G ASP* 3.7 27.8 - - - -
78G LEU* 3.8 39.3 - - + -
96G VAL* 4.5 3.8 - - + -
127G ALA* 2.8 45.0 + - + +
128G ALA 3.9 3.6 - - - +
130G ILE* 1.3 73.0 - - - +
132G THR* 1.3 57.6 + - - +
134G GLN* 3.6 17.0 - - - +
135G LEU* 2.8 34.8 + - - +
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Residues in contact with THR 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G VAL* 4.1 12.9 - - - +
112G LEU* 3.6 21.1 - - + +
113G HIS 4.9 0.9 - - - -
114G TYR* 3.5 33.5 + - + +
128G ALA 2.9 15.7 + - - -
129G ALA 3.3 9.4 - - - +
131G PHE* 1.3 76.5 - - - +
133G VAL* 1.3 64.0 + - - +
135G LEU* 3.3 1.7 + - - -
136G ASP* 3.0 22.5 + - - +
145G GLN* 3.7 33.0 - - + +
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Residues in contact with VAL 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A TYR* 4.2 15.7 - - + +
148A THR* 3.6 20.4 - - + -
167A GLU 3.8 6.7 - - - +
168A GLY* 3.6 20.0 - - - -
169A TYR* 3.8 23.6 - - + +
129G ALA 3.1 15.3 + - - +
130G ILE* 3.0 8.1 + - + +
132G THR* 1.3 75.1 - - - +
134G GLN* 1.3 63.8 + - + +
136G ASP* 3.4 1.2 + - - +
137G ASP* 3.0 43.1 + - - +
145G GLN* 4.0 9.9 - - - +
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Residues in contact with GLN 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A LEU* 4.9 0.9 - - - +
349A LEU* 4.5 3.3 - - - +
351A THR* 2.6 40.3 + - - +
355A MET* 3.6 25.3 - - - +
52G MET 6.1 0.4 - - - +
54G VAL* 4.2 13.2 + - + +
59G PHE* 3.6 13.7 - - + -
130G ILE* 2.9 31.1 + - + +
131G PHE* 3.6 23.6 - - - +
133G VAL* 1.3 80.6 - - + +
135G LEU* 1.3 59.5 + - - +
137G ASP* 3.6 8.9 - - - +
138G TYR* 3.0 27.9 + - - +
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Residues in contact with LEU 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G PHE* 3.8 25.0 - - + -
62G ALA* 3.8 24.9 - - + -
71G TRP* 4.0 24.0 - - + -
78G LEU* 4.5 9.9 - - + -
96G VAL* 4.0 11.7 - - + -
98G LEU* 4.6 4.3 - - + -
112G LEU* 3.9 24.5 - - + -
131G PHE 2.8 15.4 + - - +
132G THR 3.7 3.1 - - - +
134G GLN* 1.3 75.7 - - - +
136G ASP* 1.3 65.4 + - - +
138G TYR* 3.2 5.0 + - + +
139G LEU* 3.0 47.2 + - + +
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Residues in contact with ASP 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 3.1 16.6 - - - +
112G LEU* 3.8 10.4 - - + +
132G THR 3.0 18.3 + - - +
133G VAL 3.6 3.1 - - - +
135G LEU* 1.3 76.2 - - - +
137G ASP* 1.3 55.9 + - - +
139G LEU* 2.9 15.9 + - - +
141G GLY* 2.8 59.5 + - - -
143G ALA* 3.0 26.6 + - - +
145G GLN* 2.7 29.2 + - - +
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Residues in contact with ASP 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU 5.2 0.9 - - - +
169A TYR* 2.4 43.5 + - - -
52G MET 4.7 10.0 - - - +
53G VAL* 3.7 24.3 - - + +
133G VAL* 3.0 22.1 + - - +
134G GLN* 3.6 9.0 - - - +
136G ASP* 1.3 77.7 - - - +
138G TYR* 1.3 62.7 + - - +
140G ASN* 3.0 15.5 + - - -
141G GLY* 4.1 7.7 - - - +
145G GLN* 5.6 0.2 + - - -
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Residues in contact with TYR 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G VAL* 4.0 20.9 - - + +
54G VAL 3.4 19.3 - - - +
55G GLU* 3.7 22.1 + - - -
59G PHE* 3.4 44.9 - + + -
60G LEU* 3.5 29.5 + - + +
64G LYS* 4.1 19.5 + - - -
134G GLN 3.0 19.1 + - - +
135G LEU* 3.5 6.5 - - + +
136G ASP 3.2 0.2 - - - -
137G ASP* 1.3 76.0 - - - +
139G LEU* 1.3 69.6 - - + +
140G ASN* 3.1 12.9 + - - +
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Residues in contact with LEU 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G ALA* 4.1 19.3 - - + +
64G LYS* 4.7 4.5 - - - +
98G LEU* 4.3 13.7 - - + -
110G TYR* 3.9 50.3 - - + +
112G LEU* 5.2 0.7 - - + -
135G LEU* 3.0 34.2 + - + +
136G ASP* 2.9 9.2 + - - +
138G TYR* 1.3 89.8 - - + +
140G ASN* 1.3 73.0 + - - +
141G GLY 3.0 5.3 + - - -
142G ARG* 3.1 21.1 + - - +
143G ALA* 4.4 8.7 - - + +
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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
------------------------------------------------------------
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