Contacts of the helix formed by residues 140 - 155 (chain I) in PDB entry 3EXG
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 140 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I ASN* 5.0 9.0 - - + -
137I ILE* 3.1 34.8 + - + +
138I VAL 3.2 3.0 + - - -
139I GLY* 1.3 75.2 - - - +
141I GLN* 1.3 61.0 + - - +
142I VAL 3.4 0.5 + - - -
143I PRO* 3.6 4.4 - - - +
144I LEU* 3.5 13.6 - - + +
174I GLN* 3.4 14.9 - - - +
91J ASP* 4.1 11.4 - - - +
92J GLN* 3.3 19.0 + - - +
96J SER* 4.5 11.0 - - - +
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Residues in contact with GLN 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ILE* 3.7 15.1 - - + +
87I THR* 3.7 11.7 - - - +
88I ALA* 3.4 32.8 - - - +
135I ASN* 3.7 24.6 - - - +
137I ILE 4.1 4.5 - - - +
138I VAL* 5.0 0.2 - - - -
139I GLY 3.2 20.3 + - - +
140I ALA* 1.3 74.9 + - - +
142I VAL* 1.3 65.1 + - - +
143I PRO 3.5 0.2 - - - -
144I LEU* 3.5 9.7 - - - +
145I GLY* 2.8 26.0 + - - -
163I THR* 3.5 3.7 - - + +
164I LEU 2.9 29.2 + - - +
165I TYR* 3.7 10.9 - - - +
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Residues in contact with VAL 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I GLY* 2.8 15.5 + - - +
141I GLN* 1.3 79.4 - - - +
143I PRO* 1.4 63.5 - - + +
145I GLY* 3.2 2.4 + - - -
146I ALA* 2.9 26.0 + - - +
163I THR* 3.5 11.3 - - + +
165I TYR* 3.9 25.4 - - + -
175I ILE* 3.5 43.7 - - + -
178I ALA* 4.5 2.9 - - + -
191I PHE* 3.7 32.2 - - + -
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Residues in contact with PRO 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I GLY 3.3 13.5 - - - +
140I ALA 3.6 3.1 - - - +
142I VAL* 1.4 91.9 - - + +
144I LEU* 1.3 55.9 + - - +
146I ALA* 3.2 1.9 + - + +
147I GLY 2.9 21.8 + - - -
174I GLN* 3.4 45.1 - - + +
178I ALA* 4.2 10.5 - - + -
60J MET 4.8 0.2 - - - +
61J GLY* 3.8 15.5 - - - +
64J GLY* 3.7 24.7 - - - -
65J ILE* 3.4 13.6 - - + +
92J GLN* 4.0 2.7 - - - +
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Residues in contact with LEU 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ILE* 3.6 17.3 - - + -
135I ASN* 3.7 23.1 - - - +
140I ALA* 3.5 15.6 + - + +
141I GLN* 3.2 9.7 + - - +
143I PRO* 1.3 74.7 - - - +
145I GLY* 1.3 60.5 + - - +
147I GLY* 3.0 2.1 + - - -
148I ILE* 2.8 35.1 + - + +
64J GLY 3.5 19.7 - - - +
67J VAL* 3.9 14.4 - - + +
68J GLY* 3.7 16.6 - - - +
71J MET* 4.2 18.6 - - + -
92J GLN* 3.9 16.8 - - - +
96J SER* 4.2 12.8 - - - +
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Residues in contact with GLY 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ILE* 3.8 12.7 - - - +
141I GLN 2.8 17.2 + - - -
142I VAL 3.2 2.6 + - - -
144I LEU* 1.3 73.3 - - - +
146I ALA* 1.3 56.6 + - - +
148I ILE* 3.3 5.0 + - - -
149I ALA* 2.8 29.2 + - - +
161I CYS* 3.6 6.8 - - - -
163I THR* 3.2 24.0 - - - -
189I CYS* 4.5 0.2 - - - -
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Residues in contact with ALA 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I VAL 2.9 13.2 + - - +
143I PRO 3.2 7.8 + - - +
145I GLY* 1.3 75.7 - - - +
147I GLY* 1.3 58.0 + - - +
149I ALA* 3.1 9.1 - - - +
150I LEU* 2.7 30.3 + - - +
163I THR* 4.2 0.8 + - - -
178I ALA* 4.1 16.6 - - + +
182I ALA* 5.0 0.7 - - + -
187I LEU* 3.9 10.5 - - + +
189I CYS* 4.2 4.9 - - - -
191I PHE* 4.5 11.2 - - + -
65J ILE* 3.8 21.3 - - + -
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Residues in contact with GLY 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I PRO 2.9 12.5 + - - -
144I LEU 3.0 4.4 + - - -
146I ALA* 1.3 73.5 - - - +
148I ILE* 1.3 66.1 + - - +
150I LEU* 3.0 5.0 + - - +
151I ALA 3.0 19.4 + - - -
65J ILE* 3.3 33.8 - - - +
68J GLY* 4.0 0.2 - - - -
69J ALA* 3.5 15.0 + - - -
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Residues in contact with ILE 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I HIS* 3.5 42.0 - - + +
86I ILE* 4.4 9.4 - - + -
132I TYR* 3.4 41.5 - - + -
144I LEU* 2.8 28.5 + - + +
145I GLY* 3.7 9.4 - - - +
147I GLY* 1.3 70.6 - - - +
149I ALA* 1.3 64.6 + - - +
151I ALA* 3.2 4.9 + - - +
152I CYS* 3.2 19.5 + - - -
161I CYS* 3.8 7.6 - - + -
68J GLY* 3.7 16.7 - - - +
71J MET* 5.7 1.6 - - + -
72J ALA* 4.0 17.0 - - + -
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Residues in contact with ALA 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I GLY 2.8 14.7 + - - +
146I ALA* 3.1 10.3 - - - +
148I ILE* 1.3 76.2 - - - +
150I LEU* 1.3 62.8 + - - +
152I CYS* 2.9 23.8 + - - +
153I LYS 3.2 5.2 + - - -
161I CYS* 3.9 15.7 - - + +
187I LEU* 4.4 5.8 - - + -
188I PRO* 3.6 12.4 - - - +
189I CYS* 3.6 31.9 - - + +
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Residues in contact with LEU 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I ALA 2.7 19.0 + - - +
147I GLY* 3.0 5.4 + - - +
149I ALA* 1.3 73.1 - - - +
151I ALA* 1.3 63.7 + - - +
153I LYS* 3.5 10.1 + - + +
154I TYR* 3.0 31.2 + - + +
185I TRP* 4.2 18.6 - - + -
187I LEU* 3.6 31.9 - - + -
24J PHE* 4.3 27.6 - - + -
26J LEU* 5.4 1.3 - - + -
53J ILE* 4.6 13.5 - - + -
65J ILE* 3.9 23.3 - - + -
69J ALA* 4.7 4.3 - - + -
74J LEU* 6.0 1.3 - - + -
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Residues in contact with ALA 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I GLY 3.0 9.4 + - - +
148I ILE 3.2 10.5 + - - +
150I LEU* 1.3 76.6 - - - +
152I CYS* 1.3 63.6 + - - +
154I TYR* 2.9 16.6 + - - +
155I ASN* 3.0 19.2 + - - +
69J ALA* 4.3 5.4 - - - +
72J ALA* 3.7 26.2 - - + +
74J LEU* 3.6 28.9 - - + -
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Residues in contact with CYS 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I HIS* 3.5 33.9 - - - -
148I ILE* 3.2 17.7 + - - -
149I ALA* 2.9 11.9 + - - +
151I ALA* 1.3 71.6 - - - +
153I LYS* 1.3 69.0 + - - +
154I TYR 2.8 1.4 + - - -
155I ASN* 2.8 18.8 + - - +
156I GLY* 3.4 7.6 + - - -
157I LYS* 4.2 4.7 + - - -
158I ASP 5.3 0.6 + - - -
159I GLU* 3.4 42.4 - - + +
160I VAL 4.1 7.0 - - - -
188I PRO* 4.1 3.4 - - + -
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Residues in contact with LYS 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149I ALA 3.2 3.8 + - - +
150I LEU* 3.8 13.6 - - + +
152I CYS* 1.3 78.6 - - - +
154I TYR* 1.3 62.0 + - - +
156I GLY* 3.1 14.5 + - - -
185I TRP* 3.1 41.9 + - - +
186I LYS 4.0 9.9 - - - +
187I LEU* 4.0 9.4 - - + +
188I PRO* 4.0 21.0 - - + +
50J LYS* 5.5 0.3 + - - -
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Residues in contact with TYR 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I LEU* 3.0 23.1 + - + +
151I ALA* 2.9 16.3 + - - +
152I CYS 2.8 1.4 + - - -
153I LYS* 1.3 78.3 - - - +
155I ASN* 1.3 62.2 + - - +
156I GLY 3.3 0.9 - - - -
21J GLU* 2.6 33.5 + - + -
22J LYS* 4.1 1.9 + - + -
23J VAL 3.9 0.2 + - - -
24J PHE* 3.8 25.8 - + + +
50J LYS* 3.0 79.5 + - + +
51J ARG* 3.0 19.2 + - - -
74J LEU* 3.4 28.0 - - + -
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Residues in contact with ASN 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I ALA* 3.0 23.8 + - - +
152I CYS* 2.8 13.3 + - - +
154I TYR* 1.3 87.1 - - - +
156I GLY* 1.3 68.8 + - - +
157I LYS* 3.1 24.3 + - + +
159I GLU* 5.4 5.4 + - - +
22J LYS* 5.2 5.4 - - - +
72J ALA 5.4 4.9 + - - -
74J LEU* 3.9 15.2 - - - +
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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