Contacts of the helix formed by residues 127 - 141 (chain S) in PDB entry 5KZ5
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 ALA 127 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E TYR* 4.4 0.4 + - - -
126S GLY* 1.4 72.5 - - - -
128S THR* 1.3 59.5 + - - +
129S GLU 3.5 0.2 - - - -
130S SER* 3.4 8.3 + - - -
131S ASN* 3.0 35.5 + - - +
156S HIS* 3.9 23.3 - - + +
232S ASP* 4.2 6.1 - - - +
234S ALA* 3.8 28.9 - - + -
235S GLN* 4.8 1.6 - - - +
253S SER* 4.4 1.6 - - - -
255S SER* 4.0 8.5 + - - -
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Residues in contact with THR 128 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E TYR* 3.2 14.7 + - - +
127S ALA* 1.3 77.4 - - - +
129S GLU* 1.3 69.7 + - - +
131S ASN* 3.4 3.6 + - - +
132S ASN* 3.1 32.7 + - - -
156S HIS* 3.6 35.0 - - + -
158S CYS* 3.8 32.6 - - + +
159S VAL* 3.8 9.1 - - + +
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Residues in contact with GLU 129 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E PRO* 4.7 19.3 - - + +
118E TYR* 3.2 34.5 + - - -
124S THR* 3.7 21.5 - - + +
125S SER 3.3 6.1 + - - -
126S GLY 3.2 27.3 + - - -
128S THR* 1.3 81.5 + - - +
130S SER* 1.4 63.7 + - - +
131S ASN 3.3 0.2 - - - -
132S ASN* 3.8 11.7 - - - +
133S ILE* 3.3 23.6 + - - +
281S LEU* 3.8 21.9 - - + +
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Residues in contact with SER 130 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124S THR* 3.0 26.8 + - - +
126S GLY 3.2 10.5 + - - -
127S ALA* 3.4 6.7 + - - -
128S THR 3.3 0.4 - - - -
129S GLU* 1.4 78.2 - - - +
131S ASN* 1.4 61.1 + - - +
133S ILE* 3.3 16.4 - - - +
134S ALA* 3.4 12.6 + - - +
230S HIS* 4.6 0.9 + - - -
253S SER* 3.1 26.4 + - - -
254S ILE 4.5 2.9 + - - -
267S ALA 4.1 4.9 + - - -
268S ILE* 3.5 22.0 - - - +
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Residues in contact with ASN 131 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127S ALA* 3.0 21.6 + - - +
128S THR 3.6 4.9 - - - +
129S GLU 3.3 0.2 - - - -
130S SER* 1.4 73.4 - - - +
132S ASN* 1.4 65.3 + - - +
134S ALA* 3.5 0.5 + - - +
135S ILE* 3.0 37.3 + - + +
155S GLU* 5.2 7.5 + - - +
156S HIS* 4.9 6.1 - - - +
159S VAL* 3.9 29.1 - - + +
203S MET* 5.3 3.0 - - - +
207S ASN* 5.0 2.4 - - - +
230S HIS* 3.4 21.5 - - - -
232S ASP* 3.2 30.8 + - - +
253S SER* 3.4 6.1 + - - -
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Residues in contact with ASN 132 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128S THR* 3.1 17.9 + - - +
129S GLU* 3.8 15.4 - - - +
130S SER 3.4 0.2 - - - -
131S ASN* 1.4 79.1 - - - +
133S ILE* 1.4 61.4 + - - +
135S ILE* 5.1 0.2 - - - -
136S LYS* 3.3 37.4 + - + +
158S CYS* 5.6 2.3 - - - +
159S VAL* 4.0 17.8 - - - +
162S SER* 3.6 32.1 + - - +
281S LEU* 4.6 11.5 - - + +
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Residues in contact with ILE 133 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122S ILE* 4.4 24.0 - - + -
124S THR* 5.6 3.4 - - + -
129S GLU 3.3 12.0 + - - +
130S SER* 3.3 13.7 - - - +
132S ASN* 1.4 77.3 - - - +
134S ALA* 1.4 66.5 + - - +
136S LYS* 5.5 0.2 - - - -
137S GLY* 3.4 14.6 + - - -
268S ILE* 3.9 23.3 - - + -
277S ARG* 3.7 29.2 - - - +
279S GLU 5.5 0.2 - - - +
280S ALA* 4.3 11.0 - - + -
281S LEU* 3.6 46.3 - - + +
282S GLN 4.7 1.3 - - - +
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Residues in contact with ALA 134 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130S SER 3.4 14.7 + - - +
131S ASN 3.8 1.6 - - - +
132S ASN 3.3 0.6 - - - -
133S ILE* 1.4 81.2 - - - +
135S ILE* 1.4 60.7 + - - +
138S VAL* 3.4 30.0 + - - +
230S HIS* 3.3 33.4 - - + +
251S LEU* 3.5 12.9 - - + +
252S MET 6.1 0.7 - - - +
253S SER* 5.9 0.7 - - - +
268S ILE* 5.2 2.2 - - + -
277S ARG* 3.8 18.2 + - - +
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Residues in contact with ILE 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131S ASN* 3.0 30.0 + - + +
134S ALA* 1.4 71.0 - - - +
136S LYS* 1.4 85.7 + - + +
137S GLY 3.5 0.2 + - - -
138S VAL* 3.5 1.6 + - - -
139S ALA* 3.1 21.2 + - + +
151S THR* 5.4 1.3 - - + -
155S GLU* 3.2 27.6 - - - +
159S VAL* 4.3 6.3 - - + -
163S CYS* 5.0 6.7 - - - -
199S LEU* 3.6 35.8 - - + +
201S SER* 3.9 14.6 - - - +
230S HIS* 3.7 28.0 - - + +
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Residues in contact with LYS 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132S ASN* 3.3 31.1 + - + +
133S ILE* 5.0 0.4 - - - +
135S ILE* 1.4 89.3 - - + +
137S GLY* 1.4 62.5 + - - +
139S ALA* 3.2 15.0 + - - +
140S ARG* 3.1 40.9 + - - +
149S LEU* 5.8 2.4 - - - +
159S VAL* 5.6 0.9 - - - -
162S SER* 3.6 34.1 - - - +
163S CYS* 3.6 33.6 - - - +
166S LEU* 3.7 34.5 - - + +
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Residues in contact with GLY 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133S ILE 3.4 18.8 + - - -
135S ILE 3.4 0.6 - - - -
136S LYS* 1.4 78.6 - - - +
138S VAL* 1.4 60.5 + - - +
140S ARG* 4.6 5.6 - - - +
141S PHE* 3.4 22.5 + - - +
277S ARG* 3.9 12.6 - - - -
278S VAL* 3.5 26.8 + - - +
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Residues in contact with VAL 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134S ALA 3.4 19.3 + - - +
135S ILE 3.8 3.8 - - - +
136S LYS 3.4 0.4 - - - -
137S GLY* 1.4 73.4 - - - +
139S ALA* 1.3 64.0 + - - +
141S PHE* 3.4 15.6 + - - +
142S TYR* 3.5 11.2 + - + +
198S SER 3.7 18.8 - - - +
199S LEU* 4.0 12.3 - - + -
227S VAL* 4.8 0.2 - - + -
228S TYR* 3.7 33.4 - - + +
230S HIS* 6.0 1.8 - - + -
251S LEU* 3.5 26.7 - - + -
276S VAL* 3.8 18.6 - - + -
277S ARG* 4.2 3.5 - - + +
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Residues in contact with ALA 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135S ILE* 3.1 15.3 + - + +
136S LYS* 3.2 15.9 + - + +
138S VAL* 1.3 79.5 - - - +
140S ARG* 1.3 64.7 - - - +
143S ARG* 3.5 10.0 - - - +
149S LEU* 3.5 36.5 - - + +
166S LEU* 5.9 2.0 - - + -
171S PHE* 4.7 4.0 - - + -
198S SER* 3.3 24.4 + - - -
199S LEU* 4.6 5.2 - - + -
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Residues in contact with ARG 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136S LYS* 3.1 45.3 + - - +
137S GLY* 4.6 3.8 - - - +
139S ALA* 1.3 81.3 - - - +
141S PHE* 1.4 64.2 + - - +
143S ARG* 3.2 27.5 + - - +
166S LEU* 4.0 24.4 - - - +
169S GLU* 4.4 10.7 + - - +
171S PHE* 4.4 23.3 - - + -
278S VAL* 3.9 18.2 + - + +
279S GLU* 5.9 6.5 - - - +
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Residues in contact with PHE 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137S GLY 3.4 16.8 + - - +
138S VAL* 3.4 6.2 + - - +
140S ARG* 1.4 79.9 - - - +
142S TYR* 1.4 59.9 + - + +
143S ARG 3.7 0.3 + - - -
144S SER 5.2 0.9 + - - -
228S TYR* 3.7 29.6 - + - -
275S ARG* 3.9 18.2 - - + -
276S VAL* 3.5 23.6 - - - -
277S ARG* 3.2 34.1 - - - -
278S VAL* 3.6 19.7 - - + +
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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
------------------------------------------------------------
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