Contacts of the helix formed by residues 137 - 150 (chain C) in PDB entry 3SAJ
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 LEU 137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.9 23.1 - - + -
140A LEU* 5.8 3.8 - - + -
141A GLN* 3.6 36.1 - - + +
131C TYR* 3.8 34.1 - - + -
133C ALA* 4.5 11.4 - - + +
136C GLY* 1.3 84.8 - - - +
138C SER* 1.3 66.1 + - - +
139C VAL 3.2 3.5 + - - -
140C LEU* 3.2 19.2 + - + -
141C GLN* 3.1 37.2 + - + +
185C ASP* 6.1 0.4 - - - -
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Residues in contact with SER 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PHE* 4.7 18.6 - - - -
96C PRO 5.5 2.1 + - - -
97C VAL* 5.7 4.2 - - - -
98C ASP* 4.2 14.6 + - - +
112C GLN* 3.4 15.8 + - - +
136C GLY* 3.6 1.9 - - - -
137C LEU* 1.3 79.2 - - - +
139C VAL* 1.3 64.2 + - - +
141C GLN* 3.4 10.3 + - - +
142C ARG* 3.2 19.4 + - - +
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Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PHE* 4.0 26.9 - - + -
111C LEU* 5.9 1.6 - - + -
112C GLN* 4.1 26.0 - - + +
115C LEU* 3.8 26.5 - - + -
129C TYR* 3.1 18.4 - - + +
135C ARG* 5.3 2.0 - - - +
136C GLY 5.6 0.2 - - - -
137C LEU 3.3 0.8 - - - -
138C SER* 1.3 79.2 - - - +
140C LEU* 1.3 67.6 + - - +
142C ARG* 3.1 10.4 + - - +
143C VAL* 2.9 21.3 + - + +
185C ASP* 3.8 12.3 - - - +
213C ALA* 4.5 10.5 - - + +
214C ASN* 5.7 0.2 - - - +
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 5.9 4.9 - - + -
141A GLN* 5.8 1.8 - - + -
144A LEU* 5.0 7.4 - - + -
129C TYR* 3.4 41.7 + - + -
131C TYR* 3.7 35.2 - - + -
137C LEU* 3.2 32.0 + - + +
139C VAL* 1.3 78.3 - - - +
141C GLN* 1.3 52.5 + - + +
143C VAL* 3.2 2.1 + - - +
144C LEU* 2.8 62.9 + - + +
156C ALA* 4.1 17.3 - - + -
185C ASP* 4.5 2.3 + - - +
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Residues in contact with GLN 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 5.1 3.8 + - - +
131A TYR* 3.7 20.8 + - + +
133A ALA* 3.8 10.1 - - - +
137A LEU* 2.8 33.9 - - + +
140A LEU* 5.1 6.5 - - + -
158A ASN* 3.1 27.6 - - - +
137C LEU* 3.1 21.3 + - + +
138C SER* 3.5 11.1 + - - +
140C LEU* 1.3 76.4 - - + +
142C ARG* 1.3 58.0 + - - +
144C LEU* 3.2 5.4 + - - +
145C ASP* 3.0 37.3 + - - +
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Residues in contact with ARG 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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161A THR* 6.4 2.0 - - - -
112C GLN* 3.6 43.4 - - + +
113C GLU* 4.2 26.3 + - - +
116C ILE* 4.1 13.1 - - + +
138C SER 3.2 9.2 + - - +
139C VAL 3.1 9.8 + - - +
141C GLN* 1.3 77.4 - - - +
143C VAL* 1.3 64.9 + - - +
145C ASP* 3.5 13.7 + - - +
146C THR* 3.2 43.9 + - - +
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Residues in contact with VAL 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 4.0 19.3 - - + -
116C ILE* 4.1 22.4 - - + -
119C ILE* 4.9 4.3 - - + -
127C PHE* 4.1 21.8 - - + -
129C TYR* 3.9 34.3 - - + -
139C VAL* 2.9 15.8 + - + +
140C LEU 3.7 6.5 - - - +
142C ARG* 1.3 74.0 - - - +
144C LEU* 1.3 64.7 + - + +
146C THR* 3.1 4.2 + - - +
147C ALA* 2.8 26.0 + - - +
152C TRP* 4.7 3.6 - - + -
154C VAL* 4.4 10.3 - - + -
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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
----------------------------------------------------------
131A TYR* 4.6 4.7 - - - +
140A LEU* 4.6 10.3 - - + -
144A LEU* 3.7 31.6 - - + -
156A ALA* 3.6 37.6 + - + +
140C LEU* 2.8 39.8 + - + +
141C GLN* 3.2 6.7 + - - +
143C VAL* 1.3 73.5 - - + +
145C ASP* 1.3 58.5 + - - +
147C ALA* 3.2 7.4 - - + +
148C ALA 3.0 22.7 + - - -
154C VAL* 3.9 34.8 - - + +
156C ALA* 5.0 4.3 - - + -
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Residues in contact with ASP 145 (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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131A TYR* 3.4 13.5 + - - -
156A ALA 3.7 6.9 - - - +
157A VAL* 4.1 1.4 - - - +
158A ASN* 3.5 21.8 + - - +
161A THR* 2.9 36.2 + - - +
162A THR* 5.3 5.5 - - + +
141C GLN* 3.0 17.1 + - - +
142C ARG* 3.7 14.3 - - - +
143C VAL 3.2 0.2 - - - -
144C LEU* 1.3 75.2 - - - +
146C THR* 1.3 63.5 + - - +
148C ALA* 3.3 9.1 - - - +
149C GLU* 3.2 21.3 + - - +
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Residues in contact with THR 146 (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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116C ILE* 3.9 19.0 - - + +
142C ARG* 3.2 28.2 + - - -
143C VAL 3.1 7.8 + - - -
145C ASP* 1.3 75.3 - - - +
147C ALA* 1.3 67.4 + - - +
149C GLU* 3.2 12.6 + - - +
150C LYS* 3.0 51.8 + - + +
152C TRP* 3.7 22.9 - - + -
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Residues in contact with ALA 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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155A THR* 5.4 1.2 - - + +
143C VAL 2.8 9.8 + - - +
144C LEU* 3.2 13.5 - - + +
146C THR* 1.3 76.5 - - - +
148C ALA* 1.3 63.9 + - - +
151C ASN* 3.0 7.8 + - - -
152C TRP* 2.9 48.0 + - + +
154C VAL* 3.5 33.0 - - + +
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Residues in contact with ALA 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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155A THR* 4.1 21.2 - - + +
156A ALA 3.8 15.9 - - - +
157A VAL* 4.5 9.0 - - + -
162A THR* 6.2 1.8 - - + -
166A GLY 5.9 0.9 - - - +
169A MET* 2.7 32.9 - - - +
170A LEU* 4.2 10.4 - - + +
144C LEU 3.0 9.5 + - - +
145C ASP* 3.3 12.6 - - - +
147C ALA* 1.3 82.7 - - - +
149C GLU* 1.3 52.5 + - - +
150C LYS 3.1 1.4 + - - -
151C ASN* 3.5 2.3 + - - +
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Residues in contact with GLU 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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166A GLY* 5.6 8.5 - - - -
169A MET* 4.0 25.0 - - + +
145C ASP 3.2 9.9 + - - +
146C THR* 3.2 19.9 + - - +
148C ALA* 1.3 76.6 - - + +
150C LYS* 1.3 77.2 + - + +
151C ASN 3.8 0.2 - - - -
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Residues in contact with LYS 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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169A MET* 5.4 0.2 - - - -
172A GLN* 4.2 3.8 - - - +
116C ILE* 4.6 7.1 - - - +
120C ASP* 2.8 33.8 + - - -
125C GLN* 3.5 15.7 + - - +
146C THR* 3.0 35.8 + - + +
149C GLU* 1.3 96.2 - - + +
151C ASN* 1.3 71.5 + - - +
152C TRP* 3.2 29.4 + - + +
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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
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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