Contacts of the helix formed by residues 135 - 154 (chain C) in PDB entry 1P7L
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 PRO 135 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C TYR* 4.0 26.0 - - + -
127C THR* 3.6 8.7 - - + -
129C GLU* 3.6 5.8 - - - +
133C LEU 4.8 0.2 - - - +
134C MET* 1.3 107.1 - - + +
136C ALA* 1.3 61.9 + - - +
137C PRO* 4.4 3.6 - - + -
138C ILE* 3.6 9.6 - - + +
139C THR* 2.9 24.3 - - - +
251C TYR* 3.9 20.9 - - + +
254C MET* 4.0 27.8 - - + -
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLU* 2.6 24.7 + - - +
130C THR* 4.3 11.4 - - + -
134C MET 3.7 0.8 + - - -
135C PRO* 1.3 69.9 - - - +
137C PRO* 1.3 71.6 - - + +
139C THR* 2.3 28.9 + - - -
140C TYR* 3.0 26.4 + - + -
170C PHE* 4.3 8.5 - - + -
172C TYR* 4.4 1.6 - - - +
177C ILE* 4.5 9.4 - - + -
215C TRP* 5.1 2.2 - - + -
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Residues in contact with PRO 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 3.9 22.9 - - + +
7C SER* 3.6 26.7 - - - +
129C GLU* 3.8 0.2 - - - +
135C PRO* 3.8 7.4 - - + -
136C ALA* 1.3 94.5 - - + +
138C ILE* 1.3 62.9 + - - +
140C TYR* 3.4 1.7 + - - +
141C ALA* 3.1 23.4 + - - +
168C VAL* 5.1 2.3 - - - +
170C PHE* 3.4 36.2 - - + -
172C TYR* 3.3 22.4 - - + +
254C MET* 4.4 1.3 - - + -
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Residues in contact with ILE 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER* 4.0 5.2 + - - -
8C GLU 3.6 24.7 - - - +
9C SER* 4.5 0.9 - - - +
134C MET* 3.8 24.7 - - + -
135C PRO* 3.6 21.0 - - + +
137C PRO* 1.3 78.6 - - - +
139C THR* 1.3 69.5 + - - +
141C ALA* 3.4 1.3 + - + -
142C HIS* 3.0 51.5 + - + +
248C VAL* 3.9 11.4 - - - +
250C THR 4.6 4.5 - - - +
251C TYR 3.9 8.0 + - - +
252C GLY* 3.7 33.7 - - - +
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Residues in contact with THR 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C THR* 4.8 5.9 - - + +
132C VAL* 4.8 7.9 - - + -
134C MET* 3.7 23.6 - - + +
135C PRO 2.9 22.0 - - - +
136C ALA* 2.3 31.6 + - - -
138C ILE* 1.3 81.4 - - + +
140C TYR* 1.3 67.1 + - - +
142C HIS* 3.7 7.3 + - - +
143C ARG* 2.7 43.0 + - - +
361C GLY* 6.2 0.9 - - - -
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Residues in contact with TYR 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C THR* 5.9 3.6 - - + +
136C ALA* 3.0 28.0 + - + +
137C PRO 4.2 0.9 - - - +
139C THR* 1.3 85.7 + - - +
141C ALA* 1.3 66.7 + - - +
143C ARG* 3.2 39.8 + - - +
144C LEU* 2.9 27.9 + - - +
168C VAL* 5.3 2.5 - - + -
170C PHE* 3.4 26.2 - + + -
180C ILE* 6.1 0.2 - - + -
210C ILE* 4.1 15.2 - - + +
211C LEU* 4.3 13.9 - - + -
212C PRO* 4.0 20.5 - - + +
215C TRP* 3.2 35.0 - + - -
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER 4.7 1.8 - - - +
8C GLU* 3.9 13.7 - - - +
9C SER* 3.6 24.4 - - - +
137C PRO 3.1 17.9 + - - +
138C ILE* 3.8 4.5 - - - +
140C TYR* 1.3 76.6 - - - +
142C HIS* 1.3 64.8 + - - +
144C LEU* 3.0 18.6 + - - +
145C VAL 3.3 4.2 + - - -
166C SER* 3.0 24.9 + - - +
168C VAL* 4.5 9.8 - - + +
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Residues in contact with HIS 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER* 2.4 29.9 + - - -
134C MET* 6.1 1.3 - - + -
138C ILE* 3.0 35.8 + - + +
139C THR* 3.7 7.6 - - - +
141C ALA* 1.3 76.8 - - - +
143C ARG* 1.3 62.8 + - + +
145C VAL* 3.2 5.7 - - - +
146C GLN* 3.0 32.9 + - - +
248C VAL* 3.1 32.0 + - + -
250C THR 5.4 1.0 + - - -
357C TYR* 3.3 26.7 - - - +
358C GLY* 3.1 30.1 - - - -
360C PHE 5.3 5.2 - - - -
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Residues in contact with ARG 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C VAL* 6.4 0.4 - - - +
139C THR* 2.7 32.2 + - - +
140C TYR* 3.2 42.7 + - - +
142C HIS* 1.3 77.7 - - + +
144C LEU* 1.3 56.9 + - - +
146C GLN* 3.7 11.4 - - - +
147C ARG* 2.9 30.8 + - - +
210C ILE* 3.7 30.4 + - + +
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C TYR 2.9 16.8 + - - +
141C ALA* 3.0 7.4 + - - +
143C ARG* 1.3 73.4 - - - +
145C VAL* 1.3 66.4 + - - +
147C ARG* 3.2 3.1 + - - -
148C GLN* 3.1 18.4 + - - +
166C SER* 3.9 17.0 - - - -
168C VAL* 3.4 33.2 - - + -
183C VAL* 5.3 4.3 - - + -
184C VAL 5.0 2.9 - - - +
185C LEU* 4.1 12.3 - - + -
206C ILE* 3.5 33.3 - - + +
207C ILE* 4.0 20.2 - - + -
210C ILE* 3.7 16.6 - - + -
211C LEU* 4.1 14.4 - - + -
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Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C SER* 3.8 6.3 - - - +
10C VAL* 3.6 20.4 - - - +
11C SER* 3.6 26.9 - - - +
141C ALA 3.3 5.1 + - - +
142C HIS* 3.2 15.3 - - - +
144C LEU* 1.3 76.1 - - - +
146C GLN* 1.3 65.4 + - - +
148C GLN* 3.3 12.3 + - - +
149C ALA* 3.1 21.3 + - - +
164C ALA* 4.2 4.3 - - + +
165C LYS* 4.1 5.6 - - - +
166C SER* 3.6 34.8 - - - +
185C LEU* 5.5 1.8 - - + -
357C TYR* 3.6 14.1 + - + -
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Residues in contact with GLN 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C HIS* 3.0 26.4 + - - +
143C ARG* 3.7 11.2 - - - +
145C VAL* 1.3 79.4 - - - +
147C ARG* 1.3 61.9 + - - +
149C ALA* 3.3 4.2 + - - +
150C GLU* 3.1 21.5 + - - +
357C TYR* 3.5 45.9 + - + +
362C ARG* 5.9 3.2 + - - +
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Residues in contact with ARG 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ARG 2.9 18.4 + - - +
144C LEU 3.5 4.9 - - - +
146C GLN* 1.3 76.8 - - - +
148C GLN* 1.3 64.9 + - - +
150C GLU* 2.8 32.5 + - - +
151C VAL* 2.9 23.7 + - - +
154C ASN* 6.1 2.2 - - - +
156C THR* 5.7 0.8 - - - +
205C GLU* 2.6 48.0 + - - +
206C ILE* 3.7 22.7 - - + +
209C PRO* 4.2 16.8 - - - +
210C ILE* 3.9 20.0 - - + -
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Residues in contact with GLN 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C SER* 4.1 3.8 - - - -
144C LEU 3.1 8.7 + - - +
145C VAL* 3.5 14.9 - - - +
147C ARG* 1.3 79.9 - - - +
149C ALA* 1.3 83.7 + - - +
151C VAL* 2.9 24.7 - - - +
152C ARG* 3.2 19.3 + - - +
160C LEU* 3.5 12.5 - - + +
161C ARG 3.1 26.7 + - - -
162C PRO 4.0 0.6 + - - -
164C ALA* 3.7 21.6 - - + +
185C LEU* 5.2 4.9 - - + -
187C THR* 3.3 20.9 + - - +
206C ILE* 3.5 26.4 - - + +
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Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C SER* 5.4 1.1 - - - -
12C GLU* 3.5 13.5 - - + +
145C VAL 3.1 7.5 + - - +
146C GLN* 3.6 8.3 - - + +
147C ARG 3.1 0.2 - - - -
148C GLN* 1.3 88.6 + - - +
150C GLU* 1.3 57.6 + - - +
152C ARG* 3.4 17.5 + - - +
153C LYS* 3.0 37.2 + - + +
357C TYR* 3.5 25.1 - - - +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C GLN 3.1 12.3 + - - +
147C ARG* 2.8 28.8 + - - +
149C ALA* 1.3 74.1 - - - +
151C VAL* 1.3 59.2 + - - +
152C ARG 3.1 5.2 - - - -
153C LYS* 4.2 6.4 - - - +
154C ASN* 3.0 46.2 + - - +
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ARG* 2.9 28.5 + - + +
148C GLN* 2.9 32.5 - - - +
150C GLU* 1.3 78.4 - - - +
152C ARG* 1.3 57.1 + - - +
154C ASN* 2.9 21.1 - - - +
156C THR* 3.0 31.2 + - + -
157C LEU* 3.0 32.5 + - + -
160C LEU* 3.6 11.7 - - + -
205C GLU* 3.7 8.5 - - + -
206C ILE* 4.1 10.8 - - + -
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Residues in contact with ARG 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C SER* 5.2 0.4 + - - -
12C GLU* 4.4 7.7 - - - +
75C ILE 2.8 28.9 + - - -
76C GLY* 4.6 2.8 - - - -
148C GLN* 3.2 26.2 + - - +
149C ALA* 3.4 29.4 + - - +
150C GLU 3.1 0.4 - - - -
151C VAL* 1.3 78.1 - - - +
153C LYS* 1.3 89.0 + - - +
155C GLY* 3.1 14.2 + - - -
157C LEU 4.0 10.8 - - - +
158C PRO* 5.0 3.7 - - - +
160C LEU* 3.4 37.0 - - + +
161C ARG 3.6 14.8 - - - -
162C PRO* 3.4 30.6 + - - +
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Residues in contact with LYS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLU* 2.5 40.0 + - - -
74C GLU 3.9 16.8 + - - +
149C ALA* 3.0 29.0 + - + +
150C GLU* 4.2 6.1 - - - +
152C ARG* 1.3 89.8 - - - +
154C ASN* 1.3 60.5 + - - +
155C GLY* 3.0 6.9 + - - -
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Residues in contact with ASN 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ARG* 6.1 2.0 - - - +
150C GLU* 3.0 35.8 + - - +
151C VAL* 2.9 13.5 - - - +
153C LYS* 1.3 76.2 - - - +
155C GLY* 1.3 60.8 + - - +
156C THR* 2.5 48.4 + - - -
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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