Contacts of the helix formed by residues 110 - 123 (chain A) in PDB entry 3EW9
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 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLY 3.1 5.6 - - - -
109A SER* 1.3 80.8 - - - +
111A LYS* 1.3 65.2 + - - +
112A THR 3.3 2.2 - - - -
113A GLN* 3.3 10.0 + - - +
114A ILE* 3.1 29.0 + - - +
288A LEU* 3.9 4.3 - - - -
296A ARG* 5.0 1.3 - - - -
313A PHE* 5.5 0.7 - - - -
315A ILE* 4.9 8.9 - - - +
401A ANP 3.2 20.0 + - - -
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PHE* 3.4 19.7 - - + +
105A GLY 2.9 27.6 + - - +
106A MET 2.9 13.9 + - - -
109A SER* 3.9 8.7 - - - +
110A GLY* 1.3 74.4 - - - +
112A THR* 1.3 62.4 + - - +
114A ILE* 3.4 1.8 + - - +
115A MET* 3.3 27.7 + - - +
211A ASP* 5.1 0.4 - - - +
212A SER* 6.5 0.7 - - - -
255A THR* 3.9 21.1 - - + -
256A ASN 3.1 30.5 - - - +
257A GLN* 4.8 5.6 - - - +
288A LEU* 3.7 15.9 - - + +
401A ANP 2.7 54.2 + - - +
501A MG 4.7 0.9 - - - -
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Residues in contact with THR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 1.3 75.8 - - - +
113A GLN* 1.3 71.4 + - - +
115A MET* 3.1 4.0 + - - +
116A HIS* 2.9 52.9 + - + +
147A TYR* 3.6 8.1 - - - +
153A THR* 4.1 16.5 + - - +
211A ASP* 3.0 19.1 + - - +
255A THR* 4.7 0.2 - - - +
401A ANP 2.8 19.2 + - - +
501A MG 2.2 28.1 - - - -
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLY* 3.6 10.8 - - - +
112A THR* 1.3 79.6 - - - +
114A ILE* 1.3 63.0 + - - +
116A HIS* 3.2 3.9 + - - -
117A GLN* 3.0 21.0 + - - +
158A ARG* 2.8 44.4 + - - +
162A MET* 3.4 16.1 - - + +
315A ILE* 3.9 24.7 - - + -
320A ILE* 3.9 2.0 - - + -
401A ANP 2.8 73.2 + - - +
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 5.3 9.2 - - - -
87A LEU* 4.5 9.9 - - + -
95A ILE* 5.3 1.3 - - + -
103A PHE* 4.0 32.5 - - + -
110A GLY 3.1 8.8 + - - +
111A LYS 3.7 7.0 - - - +
113A GLN* 1.3 73.8 - - + +
115A MET* 1.3 79.9 + - + +
117A GLN* 3.3 1.4 + - - +
118A THR* 3.1 34.8 + - + +
253A LEU* 4.9 0.4 - - + -
288A LEU* 3.9 26.7 - - + -
313A PHE* 4.4 18.2 - - + -
320A ILE* 3.2 23.6 - - + -
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 4.0 16.6 - - + -
111A LYS 3.3 17.5 + - - +
112A THR* 3.1 7.8 + - - +
114A ILE* 1.3 81.6 - - + +
116A HIS* 1.3 62.2 + - - +
118A THR* 2.8 21.3 + - - -
119A CYS* 3.4 6.1 + - - -
147A TYR* 3.5 25.4 - - + +
209A ILE* 3.5 32.8 - - + +
211A ASP* 4.2 2.0 - - + -
253A LEU* 3.8 44.0 - - + +
254A VAL 4.5 1.6 - - - +
255A THR* 3.5 27.6 - - + -
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Residues in contact with HIS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A THR* 2.9 45.6 + - + +
113A GLN* 3.2 8.9 + - - +
115A MET* 1.3 76.4 - - - +
117A GLN* 1.3 62.3 + - - +
119A CYS* 3.2 22.7 + - - +
120A VAL* 3.4 10.4 + - - +
147A TYR* 3.3 21.7 + + - -
153A THR 4.0 0.6 + - - -
154A PHE* 3.7 16.2 - + - -
155A ARG* 3.0 43.6 + - + -
158A ARG* 4.1 12.2 - - + +
159A VAL* 3.6 21.5 - - + +
162A MET* 3.7 17.2 - - + +
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR 3.7 7.4 - - - +
83A GLY* 4.8 2.0 - - - -
113A GLN 3.0 6.7 + - - +
114A ILE 3.7 1.1 - - - +
116A HIS* 1.3 75.9 - - - +
118A THR* 1.3 59.8 + - + +
120A VAL* 2.9 22.2 + - - +
121A ASN* 2.8 59.7 + - - +
162A MET* 3.5 18.4 + - - +
166A ALA* 5.1 3.4 - - - +
318A LYS 4.1 2.1 + - - +
319A GLY* 3.5 10.0 - - - -
320A ILE* 2.8 63.3 + - + +
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.6 17.3 - - + +
81A SER 4.8 6.3 - - - +
82A THR* 5.0 4.3 - - - +
95A ILE* 4.0 17.7 - - + -
114A ILE* 3.1 20.0 + - + +
115A MET 2.8 19.8 + - - -
117A GLN* 1.3 77.6 - - + +
119A CYS* 1.3 56.4 + - - +
121A ASN* 4.2 8.1 - - - -
122A LEU* 2.9 30.3 + - - +
207A LEU* 3.5 14.7 - - - +
209A ILE* 3.6 5.0 - - - +
253A LEU* 3.7 21.6 - - + +
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Residues in contact with CYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A MET 3.6 13.2 - - - -
116A HIS* 3.2 12.5 + - - +
117A GLN 3.1 0.8 - - - -
118A THR* 1.3 81.2 + - - +
120A VAL* 1.3 64.5 + - - +
122A LEU* 3.5 13.2 - - - +
123A GLN* 3.8 6.8 + - - +
145A ALA* 4.3 10.4 - - - +
147A TYR* 3.9 16.6 - - - -
154A PHE* 5.2 3.4 - - - -
159A VAL* 4.8 5.8 - - + -
173A VAL* 3.5 15.6 - - + +
177A THR* 4.1 29.4 + - + +
207A LEU* 4.1 5.2 - - - -
209A ILE* 3.8 18.8 - - - -
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A HIS 3.4 8.0 + - - +
117A GLN* 2.9 15.8 + - - +
119A CYS* 1.3 76.4 - - - +
121A ASN* 1.3 65.8 + - - +
123A GLN* 3.0 19.8 + - - +
124A MET* 3.5 24.6 - - + +
159A VAL* 3.4 41.3 - - + +
162A MET* 4.0 16.8 - - + +
163A ALA* 3.8 17.3 - - + +
166A ALA* 4.1 0.2 - - + -
168A ILE* 3.6 11.8 - - + +
173A VAL* 3.8 9.2 - - + -
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Residues in contact with ASN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.8 7.3 - - + +
81A SER 2.9 28.3 + - - +
82A THR* 3.6 4.8 - - - +
83A GLY* 3.6 19.4 - - - +
117A GLN* 2.8 44.5 + - - +
118A THR* 4.0 4.6 - - - +
120A VAL* 1.3 71.9 - - - +
122A LEU* 1.3 62.0 + - - +
124A MET* 3.0 30.0 + - - +
127A LYS* 3.2 38.6 + - + +
128A ILE* 4.7 0.2 - - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TRP* 4.4 12.3 - - + -
80A LEU* 3.9 11.2 - - + +
118A THR 2.9 19.7 + - - +
119A CYS* 3.5 8.1 - - - +
120A VAL 3.1 0.2 - - - -
121A ASN* 1.3 76.0 - - - +
123A GLN* 1.3 80.0 + - - +
124A MET 3.1 4.4 + - - -
125A ARG 5.0 0.2 + - - -
128A ILE* 3.6 24.4 - - + +
143A PRO* 3.7 29.7 - - + +
144A LYS 3.7 28.3 - - - +
145A ALA* 3.9 6.7 - - + +
206A LYS* 4.3 13.0 - - + -
207A LEU* 4.1 16.6 - - + -
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Residues in contact with GLN 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A CYS 3.8 13.6 + - - +
120A VAL 3.0 10.1 + - - +
122A LEU* 1.3 97.4 - - - +
124A MET* 1.3 62.1 + - - +
125A ARG 4.1 1.4 + - - -
143A PRO* 3.0 31.7 + - - +
145A ALA* 5.7 0.4 - - - +
168A ILE* 4.3 14.2 - - + +
172A THR* 4.5 10.1 - - + +
173A VAL* 3.9 24.4 + - + +
176A ASN* 3.3 36.3 + - - +
177A THR* 5.3 0.8 + - - -
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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