Contacts of the helix formed by residues 137 - 150 (chain P) in PDB entry 3H1J
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 GLY 137 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64P PHE* 4.2 4.0 - - - -
135P PRO 3.5 2.2 - - - -
136P TRP* 1.3 78.5 - - - +
138P GLN* 1.3 67.7 + - - -
140P SER* 3.1 8.6 + - - -
141P PHE 3.0 17.7 + - - -
256P ASN* 3.2 23.7 - - - +
258P THR 3.2 12.8 - - - -
259P PRO* 4.1 0.7 - - - -
260P ALA* 3.5 7.7 - - - +
3011P GOL 4.9 0.2 - - - -
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Residues in contact with GLN 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P GLY* 1.3 70.8 - - - +
139P MET* 1.3 63.5 + - - +
141P PHE 3.4 0.2 + - - -
142P TRP* 3.0 47.6 + - - +
255P GLU* 3.5 16.2 + - + +
256P ASN* 3.5 1.2 + - - -
258P THR* 2.5 40.9 + - + +
259P PRO 3.9 0.7 - - - +
260P ALA* 3.5 1.6 - - - +
261P ASN* 2.9 35.2 + - - +
264P VAL* 2.7 30.5 + - - +
266P PRO* 3.3 26.7 - - + +
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Residues in contact with MET 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P TYR* 3.1 30.2 - - + +
138P GLN* 1.3 70.9 - - - +
140P SER* 1.3 55.1 + - - +
142P TRP* 5.1 0.9 - - - -
143P GLY* 2.7 35.3 + - - -
253P ASP* 3.0 30.5 - - + +
255P GLU* 3.9 13.0 - - + -
256P ASN* 2.7 35.6 + - + +
266P PRO* 5.2 2.2 - - - -
268P HIS 3.8 7.4 - - - +
269P ILE* 3.5 28.7 - - - -
270P LYS 3.3 31.0 - - - +
3001P SMA 4.3 8.3 - - - +
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Residues in contact with SER 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P TYR* 2.8 29.3 + - - -
133P VAL* 3.5 31.4 - - - +
135P PRO* 3.9 0.3 - - - +
136P TRP* 3.2 8.2 + - - -
137P GLY 3.1 24.7 + - - -
139P MET* 1.3 75.5 - - - +
141P PHE* 1.3 57.9 + - - +
143P GLY 3.9 0.2 - - - -
144P ALA* 2.9 31.2 + - - +
256P ASN* 2.8 16.6 + - - -
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Residues in contact with PHE 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LYS* 3.5 29.8 - - - -
136P TRP* 3.7 28.2 - + - -
137P GLY 3.0 2.6 + - - -
138P GLN 3.7 4.9 - - - +
140P SER* 1.3 79.4 - - - +
142P TRP* 1.3 88.9 + + + +
144P ALA* 3.2 8.3 + - - +
145P THR* 2.8 35.2 + - - -
171P VAL* 3.5 36.6 - - + +
172P ASP* 5.4 0.2 - - - -
260P ALA* 3.3 31.6 - - + +
262P PRO* 3.8 29.4 - - + -
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Residues in contact with TRP 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LYS* 3.8 18.8 - - + -
143E GLY 3.7 21.3 - - - -
144E CYS* 3.9 10.5 - - - -
145E VAL* 3.3 20.4 - - + -
138P GLN* 3.0 46.7 + - - +
139P MET 4.3 0.4 - - - +
141P PHE* 1.3 84.8 - + - +
143P GLY* 1.3 65.5 + - - +
145P THR* 3.3 12.3 + - + -
146P VAL* 3.0 32.1 + - + +
261P ASN 3.2 19.2 + - - -
262P PRO 3.4 17.0 - - - -
264P VAL 3.1 15.5 + - - -
265P THR* 3.4 25.4 - - + -
266P PRO* 3.8 12.8 - - + -
269P ILE* 3.7 23.8 - - + -
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Residues in contact with GLY 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P PHE* 4.0 7.6 - - - -
132P TYR* 6.1 2.5 - - - -
133P VAL* 5.9 0.2 - - - -
139P MET 2.7 22.3 + - - -
140P SER 3.9 0.2 - - - -
142P TRP* 1.3 69.4 - - - +
144P ALA* 1.3 65.5 + - - +
146P VAL* 3.1 1.4 + - - +
147P ILE* 2.9 29.9 + - - +
3001P SMA 3.5 30.2 + - - -
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Residues in contact with ALA 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P PHE* 3.7 14.6 - - - -
133P VAL* 3.7 22.2 - - + +
140P SER 2.9 19.6 + - - +
141P PHE* 3.2 6.7 - - - +
143P GLY* 1.3 75.2 - - - +
145P THR* 1.3 55.4 + - - +
148P THR* 2.5 40.6 + - + +
171P VAL* 4.4 16.2 - - + -
175P THR* 5.7 0.9 - - + -
179P PHE* 4.5 8.5 - - + -
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Residues in contact with THR 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LYS* 4.0 14.5 + - - +
142E LEU 4.0 3.8 - - - +
143E GLY* 4.0 21.5 - - - +
144E CYS 4.8 0.4 - - - +
141P PHE* 2.8 39.2 + - - -
142P TRP* 3.4 17.2 - - + -
144P ALA* 1.3 76.9 - - - +
146P VAL* 1.3 57.8 + - + +
148P THR* 3.5 1.6 + - - -
149P ASN* 3.0 44.3 + - - +
166P TRP* 4.0 5.2 - - + -
171P VAL* 3.8 16.9 - - + +
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Residues in contact with VAL 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU* 3.7 19.9 - - + +
144E CYS* 3.6 23.3 - - - -
160E CYS* 4.4 0.2 - - - -
161E HIS* 3.7 14.8 - - + -
142P TRP* 3.0 18.6 + - + +
143P GLY 3.7 2.5 - - - +
145P THR* 1.3 74.8 - - - +
147P ILE* 1.3 68.0 + - - +
149P ASN* 3.0 5.4 + - - +
150P LEU* 3.0 20.9 + - + +
3001P SMA 3.4 55.9 - - + +
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Residues in contact with ILE 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P PHE* 3.2 48.7 - - + -
143P GLY 2.9 19.5 + - - +
146P VAL* 1.3 73.1 - - - +
148P THR* 1.3 64.4 + - - +
150P LEU* 2.9 33.1 + - + +
151P PHE* 3.9 4.2 - - - -
275P PHE* 4.4 4.3 - - + -
3001P SMA 3.8 85.7 - - + +
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Residues in contact with THR 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P PHE* 4.2 2.7 - - + -
144P ALA* 2.5 25.2 + - + +
145P THR 3.5 1.6 + - - -
147P ILE* 1.3 77.3 - - - +
149P ASN* 1.3 63.1 + - - +
150P LEU 3.1 1.2 + - - -
151P PHE* 3.2 28.4 + - - +
162P VAL* 3.9 10.0 - - - +
165P ALA* 3.8 14.7 - - + +
166P TRP* 2.7 32.1 + - - +
179P PHE* 3.7 25.1 - - + -
3001P SMA 3.7 23.1 - - + -
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Residues in contact with ASN 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU* 3.0 39.7 - - + +
143E GLY* 3.6 7.6 + - - -
3103E UNL 3.9 6.1 + - - -
145P THR* 3.0 19.4 + - - +
146P VAL 3.0 7.9 + - - +
148P THR* 1.3 79.9 + - - +
150P LEU* 1.3 61.3 + - - +
151P PHE 3.0 0.4 - - - -
152P SER* 2.5 39.3 + - - -
162P VAL* 4.3 5.0 - - - +
166P TRP* 3.9 17.3 - - - -
3104P UNL 2.8 28.6 + - - -
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Residues in contact with LEU 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU* 3.6 26.9 - - + -
146P VAL* 3.0 11.5 + - + +
147P ILE* 2.9 41.1 + - + +
149P ASN* 1.3 77.4 - - - +
151P PHE* 1.3 67.5 + - + +
153P ALA* 3.1 23.4 + - - +
282P LEU* 3.7 23.6 - - + -
292P VAL* 4.0 23.1 - - + +
295P LEU* 3.9 20.0 - - + -
3001P SMA 4.8 17.9 - - + +
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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