Contacts of the strand formed by residues 154 - 165 (chain S) in PDB entry 3J7Y
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 VAL 154 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129S ARG* 3.6 4.0 + - - -
133S VAL* 4.0 22.6 - - + +
136S VAL* 3.6 43.3 - - + -
143S LEU* 5.0 0.4 - - + -
149S LEU* 4.2 6.5 - - + -
150S GLY 3.6 5.6 + - - +
151S LYS* 3.1 19.0 - - - +
153S LEU* 1.3 100.8 - - + +
155S ARG* 1.3 70.5 + - - +
198S ILE* 4.0 16.2 - - + -
199S GLU 3.5 13.0 - - - +
200S ILE* 4.1 5.8 - - + -
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Residues in contact with ARG 155 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129S ARG* 3.3 50.3 - - + +
130S LEU 5.0 1.8 - - - -
133S VAL* 5.4 1.8 - - - -
151S LYS 4.7 0.2 - - - +
154S VAL* 1.3 80.0 - - - +
156S VAL* 1.3 66.6 + - - +
157S GLU* 2.7 40.0 + - - +
197S SER 3.8 0.7 - - - +
198S ILE* 3.6 1.7 - - - -
199S GLU* 3.0 74.8 + - - +
52j ALA* 4.5 12.1 + - - +
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Residues in contact with VAL 156 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97S ALA* 3.9 17.0 - - + -
99S VAL* 4.0 6.1 - - + -
108S VAL* 5.5 1.1 - - + -
129S ARG* 3.4 4.9 - - - +
130S LEU* 2.8 63.2 + - + +
133S VAL* 3.4 28.0 - - + -
154S VAL* 4.8 1.1 - - + -
155S ARG* 1.3 76.5 - - - +
157S GLU* 1.3 65.3 + - - +
195S ILE* 3.9 27.1 - - + -
197S SER 3.5 4.3 - - - +
198S ILE* 4.2 14.4 - - + -
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Residues in contact with GLU 157 (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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127S ARG* 3.0 42.4 + - - +
128S ILE 3.2 6.7 - - - -
129S ARG* 3.9 9.5 - - - +
155S ARG* 2.7 47.5 + - - +
156S VAL* 1.3 74.2 - - - +
158S ALA* 1.3 60.4 + - - +
195S ILE* 3.4 7.6 - - - +
196S ASN* 2.8 23.8 + - - -
197S SER* 2.8 27.4 + - - +
199S GLU* 5.4 0.4 - - - +
52j ALA* 3.3 26.3 - - - +
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Residues in contact with ALA 158 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127S ARG* 3.6 0.6 - - - -
128S ILE* 2.8 45.1 + - + +
130S LEU* 4.1 22.7 - - + -
157S GLU* 1.3 76.2 - - - +
159S THR* 1.3 59.5 + - - +
193S LEU* 4.1 18.6 - - + -
194S ARG 3.3 11.2 - - - +
195S ILE* 4.1 15.3 - - + -
196S ASN* 3.6 3.3 + - - -
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Residues in contact with THR 159 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125S GLY* 4.4 10.5 - - - +
126S GLU 3.5 7.0 - - - +
127S ARG* 3.7 29.8 - - + +
158S ALA* 1.3 71.7 - - - +
160S VAL* 1.3 64.8 + - - +
161S ILE* 3.3 0.9 + - - +
193S LEU* 3.6 2.1 - - - -
194S ARG* 2.8 39.0 + - - +
196S ASN* 3.0 35.5 + - - +
18b GLY* 3.2 22.6 + - - +
22b TYR* 6.1 2.5 - - + -
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Residues in contact with VAL 160 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120S LEU* 4.7 1.8 - - + -
122S LEU* 3.9 24.2 - - + +
123S ALA 4.2 10.3 - - - +
124S CYS* 3.4 19.2 - - - +
125S GLY* 2.8 29.5 + - - -
126S GLU 3.2 12.1 + - - +
128S ILE* 3.6 19.1 - - + -
159S THR* 1.3 71.3 - - - +
161S ILE* 1.3 61.1 - - - +
162S GLU 4.3 7.6 - - - +
163S LYS* 4.6 8.3 - - + -
191S THR* 4.8 7.4 - - + -
192S VAL 3.7 10.1 - - - +
193S LEU* 3.6 22.7 - - + -
22b TYR* 4.6 1.2 - - - +
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Residues in contact with ILE 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113S LEU* 3.4 22.4 - - + -
124S CYS* 3.2 7.1 - - - -
159S THR 3.3 0.6 + - - +
160S VAL* 1.3 72.4 - - - +
162S GLU* 1.3 76.2 + - + +
192S VAL* 2.8 19.6 + - + +
194S ARG* 3.7 25.8 - - + -
13b SER* 3.1 33.7 - - - +
17b ASN* 4.1 24.7 - - + +
18b GLY* 4.0 15.0 - - - +
22b TYR* 3.0 33.8 + - - -
25b GLN* 6.2 0.2 - - + -
106b ASP 4.4 0.2 - - - +
108b SER* 5.6 3.1 - - - -
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Residues in contact with GLU 162 (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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124S CYS* 3.5 6.0 - - - -
160S VAL* 4.3 1.3 - - - +
161S ILE* 1.3 89.3 - - + +
163S LYS* 1.3 63.1 + - - +
164S THR* 3.2 17.9 + - + +
191S THR* 3.4 2.9 - - - -
192S VAL* 2.8 58.6 + - + +
9b ARG* 4.8 9.4 + - - -
11b LEU* 5.3 1.0 - - - +
12b ALA 4.2 13.7 - - - +
13b SER* 4.8 2.8 + - - -
106b ASP* 3.9 12.6 - - - +
107b GLN* 4.2 0.7 - - - -
108b SER* 3.1 39.9 + - - +
110b LEU* 5.2 0.3 - - - +
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Residues in contact with LYS 163 (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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119S GLU* 3.5 31.7 + - + -
120S LEU* 5.7 0.2 - - - -
121S ASP* 3.7 23.9 + - - +
122S LEU 3.4 27.3 + - - +
123S ALA* 5.4 0.2 - - - -
124S CYS* 3.8 7.0 - - - -
160S VAL* 4.6 2.2 - - + -
162S GLU* 1.3 73.9 - - - +
164S THR* 1.3 65.7 + - - +
190S GLN 3.4 8.7 - - - +
191S THR* 4.0 20.6 - - + -
102b GLN* 6.0 0.2 - - - +
103b LYS* 4.4 4.7 - - - +
106b ASP* 3.1 36.7 + - + +
107b GLN* 3.5 18.2 + - - +
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Residues in contact with THR 164 (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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162S GLU* 3.2 33.9 - - + +
163S LYS* 1.3 81.3 - - - +
165S GLU* 1.3 67.3 + - - +
189S PRO* 3.4 6.9 - - - +
190S GLN* 2.8 55.4 + - - +
192S VAL* 5.3 4.5 - - + +
103b LYS* 5.4 5.4 - - - -
107b GLN* 3.7 21.1 - - + +
112b VAL* 6.1 1.8 - - - -
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Residues in contact with GLU 165 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164S THR* 1.3 88.3 + - - +
166S SER* 1.3 69.1 + - - +
187S THR* 3.3 35.3 + - - +
188S THR 3.9 2.9 - - - -
189S PRO* 4.3 6.1 - - + -
190S GLN* 4.7 1.9 - - - +
103b LYS* 2.8 42.3 + - + +
107b GLN* 4.9 3.4 - - - +
112b VAL* 4.7 14.6 - - + +
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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