Contacts of the helix formed by residues 94 - 112 (chain G) in PDB entry 1P8Z
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 94 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65G GLY 4.3 0.2 + - - -
92G GLU 3.7 2.4 + - - -
93G CYS* 1.3 74.8 - - - +
95G GLN* 1.3 68.5 + - - +
96G ASP* 2.8 22.7 + - - -
97G GLU* 2.8 35.1 + - - +
98G SER* 3.1 12.5 + - - -
147G SER* 3.5 19.9 + - - -
149G PHE* 5.9 0.9 - - - -
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Residues in contact with GLN 95 (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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25A ASP* 5.6 2.2 + - - +
144A ALA* 3.3 30.9 - - - +
332A PRO* 6.0 0.2 - - - +
334A GLU* 2.7 34.2 + - - +
338A SER* 5.6 1.2 + - - -
341A ILE* 3.7 31.2 - - + +
345A ILE* 3.7 2.8 - - + +
93G CYS 4.0 0.6 + - - -
94G SER* 1.3 73.3 - - - +
96G ASP* 1.3 58.1 + - - +
98G SER* 3.0 8.7 + - - +
99G GLY* 2.8 28.9 + - - -
149G PHE* 4.4 10.9 - - + -
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Residues in contact with ASP 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 3.5 16.0 - - - +
46G VAL* 4.8 0.5 - - - +
48G LYS* 5.4 1.0 + - - -
49G PHE* 3.5 29.5 + - + -
94G SER* 2.8 26.9 + - - -
95G GLN* 1.3 78.0 - - - +
97G GLU* 1.3 66.7 + - - +
99G GLY 3.9 0.7 - - - -
100G ALA* 3.2 26.3 + - - +
147G SER* 2.9 17.7 + - - -
148G GLY* 3.0 24.1 + - - -
149G PHE* 3.6 23.2 - - + -
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Residues in contact with GLU 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G VAL* 4.0 21.1 - - + +
48G LYS 5.5 2.6 + - - +
65G GLY 3.2 6.2 - - - +
66G ASP* 4.0 5.3 - - - -
67G ALA* 3.8 18.6 - - + +
93G CYS* 3.5 3.4 - - + +
94G SER* 2.8 38.2 + - - +
96G ASP* 1.3 85.6 - - - +
98G SER* 1.3 55.2 + - - +
99G GLY 3.1 1.3 - - - -
100G ALA* 3.0 3.1 + - - +
101G ALA* 2.8 35.2 + - - +
145G VAL* 3.5 19.6 - - - +
146G ALA 4.2 7.3 - - - +
147G SER* 5.0 0.2 - - - -
1003G CA 2.6 29.8 - - - -
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Residues in contact with SER 98 (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 1.2 + - - -
145A SER 5.2 1.1 - - - -
146A GLY* 3.5 17.8 + - - -
67G ALA* 4.2 2.4 - - - +
89G LEU* 3.6 33.5 - - - +
93G CYS* 3.8 15.2 - - - -
94G SER 3.1 6.2 + - - -
95G GLN* 3.0 18.9 + - - +
97G GLU* 1.3 77.7 - - - +
99G GLY* 1.3 62.2 + - - +
101G ALA* 3.8 1.4 - - - +
102G ALA* 3.1 22.3 + - - +
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Residues in contact with GLY 99 (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 3.5 22.3 - - - +
144A ALA 5.0 0.9 - - - -
146A GLY* 4.4 0.7 - - - -
345A ILE* 4.1 17.0 - - - -
95G GLN 2.8 17.4 + - - -
98G SER* 1.3 80.7 + - - +
100G ALA* 1.3 55.3 + - - +
102G ALA* 3.2 3.5 + - - +
103G ILE* 2.9 33.4 + - - +
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Residues in contact with ALA 100 (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* 3.9 7.2 - - + +
349A LEU* 3.7 27.1 - - + -
46G VAL* 3.9 18.8 - - + -
49G PHE* 5.0 1.8 - - + -
96G ASP 3.2 20.1 + - - +
97G GLU 3.0 5.0 + - - +
99G GLY* 1.3 73.8 - - - +
101G ALA* 1.3 60.4 + - - +
103G ILE* 3.9 2.4 - - - +
104G PHE* 2.7 42.1 + - + -
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Residues in contact with ALA 101 (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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46G VAL* 3.8 11.8 - - + +
67G ALA* 4.1 17.5 - - + -
68G TYR 4.2 9.0 - - - +
69G VAL* 4.0 6.6 - - - +
87G TYR* 4.2 16.8 - - + -
89G LEU* 4.3 5.8 - - + -
97G GLU 2.8 19.5 + - - +
98G SER 3.8 5.2 - - - +
100G ALA* 1.3 72.5 - - - +
102G ALA* 1.3 64.7 + - - +
104G PHE* 3.8 1.6 - - - +
105G THR* 3.0 28.5 + - - -
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Residues in contact with ALA 102 (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* 4.7 6.3 - - + +
146A GLY* 3.9 3.8 - - - -
147A ARG 3.7 33.9 - - - +
148A THR* 3.3 22.8 - - + +
87G TYR* 4.2 9.7 - - + -
98G SER 3.1 11.7 + - - +
99G GLY* 3.5 8.3 - - - +
101G ALA* 1.3 81.9 - - - +
103G ILE* 1.3 63.7 + - - +
105G THR* 3.3 0.9 + - - -
106G VAL* 3.2 16.7 + - - +
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Residues in contact with ILE 103 (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* 3.5 44.4 - - + -
342A GLY 4.4 1.8 - - - +
345A ILE* 3.9 15.0 - - + -
346A LEU* 3.8 40.2 - - + +
349A LEU* 3.4 23.8 - - + -
99G GLY 2.9 21.8 + - - +
100G ALA 3.2 0.4 + - - +
102G ALA* 1.3 72.8 - - - +
104G PHE* 1.3 67.0 + - - +
106G VAL* 3.2 7.8 + - + +
107G GLN* 3.0 36.4 + - + +
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Residues in contact with PHE 104 (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* 3.7 15.9 - - + -
350A SER* 4.4 2.2 - - - -
351A THR* 3.5 30.1 - - + -
32G PHE* 4.3 2.8 - + - -
46G VAL* 3.9 14.4 - - + -
49G PHE 3.7 21.5 - - - -
50G ASP* 3.9 25.1 - - - -
51G LEU* 3.6 37.9 - - + -
69G VAL* 4.3 8.1 - - + -
100G ALA* 2.7 36.6 + - + +
101G ALA 3.8 3.4 - - - +
103G ILE* 1.3 73.3 - - - +
105G THR* 1.3 52.3 + - - +
107G GLN* 3.1 16.3 + - - +
108G LEU* 2.8 38.5 + - - +
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Residues in contact with THR 105 (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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148A THR* 4.2 0.9 - - + -
69G VAL* 4.1 11.4 - - - +
85G LEU* 3.9 17.4 - - + +
86G HIS 4.8 0.3 - - - -
87G TYR* 3.4 35.5 + - + +
101G ALA 3.0 15.0 + - - -
102G ALA 3.3 10.1 - - - -
104G PHE* 1.3 77.5 - - - +
106G VAL* 1.3 63.0 + - - +
108G LEU* 3.7 5.8 - - - +
109G ASP* 2.9 25.8 + - - +
118G GLN* 3.5 35.2 - - + +
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Residues in contact with VAL 106 (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* 3.8 22.4 - - + +
148A THR* 3.8 24.0 - - + -
167A GLU 3.8 3.6 - - - +
168A GLY* 3.7 21.3 - - - -
169A TYR* 4.0 19.3 - - + +
102G ALA 3.2 3.5 + - - +
103G ILE* 3.2 9.2 + - + +
105G THR* 1.3 77.8 - - - +
107G GLN* 1.3 58.7 + - + +
109G ASP* 3.7 1.4 - - - +
110G ASP* 2.9 41.3 + - - +
118G GLN* 3.8 14.8 - - - +
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Residues in contact with GLN 107 (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* 4.5 1.6 - - - +
349A LEU* 4.4 1.6 - - - +
351A THR* 2.4 43.5 + - - +
352A PHE* 5.0 0.5 + - - +
355A MET* 2.9 37.3 - - + +
27G VAL* 5.4 3.3 - - + +
32G PHE* 3.5 12.6 - - + -
103G ILE* 3.0 33.1 + - + +
104G PHE* 3.7 17.8 - - - +
106G VAL* 1.3 77.2 - - + +
108G LEU* 1.3 62.3 + - - +
110G ASP* 3.4 10.8 + - - +
111G TYR* 2.8 28.9 + - - +
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Residues in contact with LEU 108 (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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31G GLU 5.3 0.2 - - - +
32G PHE* 3.7 27.1 - - + +
35G ALA* 3.6 28.9 - - + -
44G TRP* 3.9 25.4 - - + -
51G LEU* 4.5 13.9 - - + -
69G VAL* 4.2 9.4 - - + -
71G LEU* 5.2 1.3 - - + -
85G LEU* 3.9 29.2 - - + -
104G PHE 2.8 19.4 + - - +
105G THR* 3.7 3.8 - - - +
107G GLN* 1.3 71.8 - - - +
109G ASP* 1.3 61.1 + - - +
111G TYR* 3.2 4.3 + - + +
112G LEU* 2.8 43.3 + - + +
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Residues in contact with ASP 109 (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* 3.4 2.9 - - - +
85G LEU* 3.9 12.9 - - + +
105G THR 2.9 19.3 + - - +
106G VAL 3.7 2.7 - - - +
108G LEU* 1.3 74.7 - - - +
110G ASP* 1.3 59.7 + - - +
112G LEU* 3.1 10.9 + - - -
114G GLY* 2.5 51.4 + - - -
116G ALA* 3.0 17.9 + - - +
118G GLN* 2.5 26.1 - - - +
1002G CD 2.6 28.3 - - - -
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Residues in contact with ASP 110 (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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169A TYR* 2.6 40.7 + - - -
355A MET* 6.1 1.4 - - - +
26G VAL 6.3 0.9 - - - +
106G VAL* 2.9 33.5 + - - +
107G GLN* 3.5 10.7 - - - +
108G LEU 3.3 0.2 - - - -
109G ASP* 1.3 76.6 - - - +
111G TYR* 1.3 63.7 + - - +
113G ASN* 2.9 17.9 + - - -
114G GLY* 4.2 5.4 - - - +
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Residues in contact with TYR 111 (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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26G VAL* 4.3 21.8 - - + +
27G VAL* 3.9 30.7 + - + -
32G PHE* 3.2 52.9 - + + -
33G LEU* 3.6 24.1 - - - +
35G ALA 5.8 0.4 - - - -
37G LYS* 6.1 4.6 - - - -
107G GLN 2.8 15.6 + - - +
108G LEU* 3.3 10.8 - - + +
109G ASP 3.1 0.2 - - - -
110G ASP* 1.3 77.4 - - - +
112G LEU* 1.3 71.2 + - + +
113G ASN* 3.0 12.1 + - - +
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Residues in contact with LEU 112 (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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35G ALA* 4.1 22.9 - - + +
71G LEU* 4.3 21.8 - - + -
83G TYR* 4.0 49.0 - - + +
85G LEU* 4.8 0.7 - - + -
108G LEU* 2.8 29.3 + - + +
109G ASP* 3.1 5.1 + - - +
111G TYR* 1.3 88.9 - - + +
113G ASN* 1.3 65.4 + - - +
114G GLY 3.0 9.5 + - - +
115G ARG* 3.0 17.4 + - - +
116G ALA* 4.5 7.6 - - + +
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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