Contacts of the helix formed by residues 123 - 133 (chain G) in PDB entry 4PHZ
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 123 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39F LEU* 4.3 9.6 - - - -
40F GLY* 4.7 2.5 - - - -
43F HIS* 2.8 29.9 + - - -
104F GLY* 3.6 19.8 + - - -
108F ASN* 4.5 0.4 - - - -
118G ILE 3.7 1.2 + - - -
119G TYR* 2.9 32.7 + - - -
122G ALA* 1.3 80.3 - - - +
124G PHE* 1.3 58.6 + - - +
125G PHE 3.6 0.4 - - - -
126G THR 3.4 0.4 + - - -
127G GLU* 2.9 35.9 + - - +
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Residues in contact with PHE 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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104F GLY 5.8 0.4 - - - -
107F ILE* 4.2 14.8 - - + -
108F ASN* 2.9 22.3 - - + +
111F VAL* 3.8 26.0 - - + -
112F ASN* 3.7 18.8 - - - -
39G ARG* 3.8 20.9 - - + -
119G TYR* 3.1 27.3 + + + -
120G TRP* 3.2 42.4 + + + +
123G SER* 1.3 78.8 - - - +
125G PHE* 1.3 94.5 + + - +
128G GLN* 3.1 22.2 + - - +
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Residues in contact with PHE 125 (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 TYR* 3.5 39.5 - + - -
38G VAL* 4.2 8.3 - - + -
39G ARG* 4.7 0.9 - - + -
42G GLU* 3.3 22.0 - - - -
120G TRP* 2.9 41.0 + + - +
121G GLY 4.6 0.2 - - - +
124G PHE* 1.3 96.3 - + - +
126G THR* 1.3 62.5 + - - +
128G GLN* 3.6 20.3 - - - +
129G ASP* 3.8 10.0 + - - +
145G SER* 4.2 2.3 + - - +
148G ILE* 3.6 21.1 - - + -
149G GLU* 3.4 28.1 - - - +
153G SER* 3.8 26.5 - - - +
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Residues in contact with THR 126 (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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44F VAL* 4.0 12.3 - - + -
47F MET* 3.2 35.8 - - + +
48F LEU* 5.7 3.1 - - + -
121G GLY 2.8 21.0 + - - -
122G ALA 3.5 21.3 - - - +
123G SER 3.4 0.6 + - - -
124G PHE 3.2 0.6 - - - -
125G PHE* 1.3 78.1 - - - +
127G GLU* 1.3 63.4 + - - +
128G GLN 3.1 1.8 - - - -
129G ASP* 3.6 14.7 + - - +
149G GLU* 3.2 16.9 + - - +
154G TYR* 3.0 18.5 + - - +
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Residues in contact with GLU 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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43F HIS* 3.2 39.9 + - + +
47F MET* 3.9 24.6 - - + +
55F PHE* 3.7 13.2 - - + -
105F GLU* 3.7 2.3 - - - +
108F ASN* 3.0 36.4 + - - +
109F ARG* 3.0 40.2 + - - -
113F PHE* 3.4 19.0 - - - -
123G SER 2.9 9.5 + - - +
126G THR* 1.3 75.1 - - - +
128G GLN* 1.3 62.5 + - - +
129G ASP 3.3 0.2 - - - -
130G GLY* 3.3 9.6 + - - -
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Residues in contact with GLN 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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108F ASN* 3.7 8.3 + - - +
112F ASN* 3.0 34.5 + - + +
116F TRP* 3.7 24.6 - - + -
39G ARG* 3.7 6.7 - - - +
42G GLU* 2.8 38.5 + - - +
124G PHE* 3.1 23.9 + - - +
125G PHE* 3.6 18.4 - - - -
126G THR 3.1 0.6 - - - -
127G GLU* 1.3 77.5 - - - +
129G ASP* 1.3 58.4 + - - +
131G THR* 2.9 34.4 + - - +
132G TRP* 3.3 2.3 + - - +
145G SER* 3.7 14.3 + - - +
148G ILE* 5.3 0.5 - - - +
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Residues in contact with ASP 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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125G PHE 3.8 2.5 + - - +
126G THR 3.6 9.8 + - - +
128G GLN* 1.3 78.6 - - - +
130G GLY* 1.3 60.8 + - - +
132G TRP* 3.4 4.5 + - - +
133G HIS* 2.8 40.9 + - - -
143G THR* 4.3 1.6 + - - -
145G SER* 3.1 28.0 + - - +
146G HIS* 3.1 23.8 + - - -
149G GLU* 3.4 19.7 - - - +
150G PHE* 4.8 0.9 - - - -
301G CU 2.4 28.2 - - - -
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Residues in contact with GLY 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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47F MET* 4.7 6.0 - - - +
55F PHE* 4.1 22.8 - - - -
56F TRP* 4.8 2.3 - - - -
113F PHE* 4.3 6.6 - - - -
126G THR 3.9 2.6 + - - -
127G GLU 3.3 11.9 + - - -
128G GLN 3.0 2.2 + - - -
129G ASP* 1.3 79.5 - - - +
131G THR* 1.3 56.9 + - - +
133G HIS* 3.9 12.1 - - - +
134G MET* 3.7 20.4 - - - +
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Residues in contact with THR 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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112F ASN* 4.0 19.5 - - + +
113F PHE* 3.4 31.2 - - + -
116F TRP* 4.3 8.7 - - + -
117F THR* 2.7 35.6 + - + +
119F PHE* 3.4 10.2 - - - -
127G GLU 3.9 2.0 + - - -
128G GLN 2.9 25.2 + - - +
130G GLY* 1.3 74.1 - - - +
132G TRP* 1.3 62.7 + - - +
133G HIS 3.2 1.6 - - - -
134G MET* 3.1 16.9 + - - +
135G THR* 3.4 13.7 + - - -
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Residues in contact with TRP 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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116F TRP* 3.4 41.5 - + + -
117F THR* 4.3 3.4 - - + -
46G GLY* 3.6 25.8 - - - -
47G TRP* 4.4 12.1 - + - -
50G GLY 3.1 22.7 - - - -
51G LEU* 3.9 12.1 - - + -
128G GLN 3.3 2.5 + - - +
129G ASP* 3.9 9.0 - - - +
131G THR* 1.3 79.9 - - - +
133G HIS* 1.3 64.9 + + - +
135G THR* 3.1 29.7 + - + -
136G VAL* 3.3 41.5 + - + +
143G THR* 3.9 19.7 - - + -
144G PRO* 3.5 25.3 - - + +
145G SER* 4.1 20.0 - - - -
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Residues in contact with HIS 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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196F THR* 3.1 5.2 + - - -
197F SER* 3.1 23.7 + - - +
129G ASP* 2.8 38.1 + - - +
130G GLY* 3.9 11.0 - - - +
131G THR 3.2 0.2 - - - -
132G TRP* 1.3 77.6 - + - +
134G MET* 1.3 68.8 + - + +
135G THR 3.2 0.9 - - - -
136G VAL* 3.1 9.8 - - - +
138G ARG* 3.5 36.5 - - - -
143G THR* 5.9 0.9 - - + -
146G HIS* 3.8 3.6 - + - -
301G CU 2.3 30.9 - - - -
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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