Contacts of the helix formed by residues 121 - 132 (chain A) in PDB entry 1EYN
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ARG* 6.0 7.4 - - - +
119A ALA 4.8 0.4 - - - +
120A ARG* 1.3 89.8 - - + +
122A VAL* 1.3 61.3 + - - +
123A ASP 3.2 1.0 + - - -
124A LEU* 3.4 14.2 + - - +
125A HIS* 3.3 17.9 - - - +
162A SER* 5.5 1.4 + - - -
550A 2AN 5.2 10.3 - - - +
551A GOL 5.2 16.2 - - - +
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Residues in contact with VAL 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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94A ILE* 4.0 30.5 - - + -
97A LEU* 6.0 0.2 - - + -
111A LEU* 4.5 22.0 - - + -
120A ARG* 4.1 16.2 - - + +
121A PRO* 1.3 77.5 - - - +
123A ASP* 1.3 77.3 + - - +
125A HIS* 3.0 14.2 + - + +
126A ILE* 2.9 42.3 + - + +
138A LEU* 6.0 0.4 - - + -
143A VAL* 4.9 3.1 - - + -
550A 2AN 4.3 13.7 + - - +
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Residues in contact with ASP 123 (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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118A GLY 3.4 7.7 - - - +
119A ALA* 3.2 13.0 - - - +
120A ARG* 2.8 37.7 + - - +
122A VAL* 1.3 86.6 - - - +
124A LEU* 1.3 59.0 + - + +
126A ILE* 3.2 12.6 + - - +
127A PHE* 2.8 28.5 + - - +
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Residues in contact with LEU 124 (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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120A ARG 5.8 0.2 - - - +
121A PRO 3.4 9.3 + - - +
122A VAL 3.3 1.0 - - - -
123A ASP* 1.3 75.6 - - + +
125A HIS* 1.3 64.7 + - - +
127A PHE* 3.6 21.5 - - + +
128A GLY* 3.1 17.7 + - - -
158A MET* 4.2 7.5 - - + +
159A ASP* 3.6 26.7 - - - +
160A LYS* 3.9 32.1 - - + +
162A SER* 3.8 25.8 - - - +
165A ALA* 3.5 21.1 - - + +
169A ILE* 4.0 4.5 - - - +
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Residues in contact with HIS 125 (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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94A ILE* 3.8 30.6 - - + +
95A TRP* 4.1 2.2 - - - -
97A LEU* 5.9 3.1 - - + -
121A PRO* 3.3 22.9 + - - +
122A VAL* 3.0 19.4 + - + +
124A LEU* 1.3 74.6 - - - +
126A ILE* 1.3 66.9 + - + +
128A GLY* 3.3 2.1 + - - -
129A LEU* 3.0 31.4 + - + +
162A SER* 5.0 1.6 + - - -
164A GLY* 3.1 38.1 + - - -
165A ALA* 3.6 10.6 + - + +
168A THR* 2.7 34.2 + - + +
169A ILE* 5.3 0.7 - - - -
551A GOL 4.2 11.4 + - - -
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Residues in contact with ILE 126 (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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97A LEU* 5.7 1.8 - - + -
122A VAL* 2.9 33.4 + - + +
123A ASP* 3.5 13.2 - - - +
125A HIS* 1.3 74.3 - - + +
127A PHE* 1.3 68.8 + - - +
129A LEU* 3.2 4.0 + - - +
130A GLU* 2.9 47.4 + - - +
136A ILE* 3.9 35.0 - - + -
138A LEU* 4.2 20.4 - - + -
143A VAL* 4.1 18.6 - - + -
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Residues in contact with PHE 127 (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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123A ASP 2.8 17.0 + - - +
124A LEU* 3.6 24.9 - - + +
126A ILE* 1.3 81.0 - - - +
128A GLY* 1.3 61.7 + - - +
130A GLU* 3.3 9.8 + - - +
131A LYS* 3.0 60.8 + - + +
156A ILE* 3.7 19.1 - - + -
157A VAL 3.5 29.2 - - - -
158A MET* 4.6 6.1 - - + -
159A ASP 5.4 0.4 - - - -
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Residues in contact with GLY 128 (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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124A LEU 3.1 7.9 + - - -
125A HIS 3.8 0.2 - - - -
126A ILE 3.3 0.2 - - - -
127A PHE* 1.3 87.1 - - - +
129A LEU* 1.3 62.7 + - - +
131A LYS* 3.1 9.3 + - - +
132A LEU* 3.1 26.0 + - - +
156A ILE* 3.9 4.7 - - - +
169A ILE* 3.6 31.9 - - - -
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Residues in contact with LEU 129 (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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97A LEU* 3.8 35.4 - - + -
98A GLY* 4.1 9.4 - - - -
101A VAL* 4.3 13.0 - - + -
125A HIS* 3.0 22.9 + - + +
126A ILE 3.2 2.7 + - - +
128A GLY* 1.3 75.3 - - - +
130A GLU* 1.3 62.0 + - - +
132A LEU* 3.1 19.3 + - + +
133A GLY 3.3 0.3 + - - -
134A ALA* 3.0 32.1 + - + +
136A ILE* 4.2 11.0 - - + -
151A LEU* 4.9 2.2 - - + -
168A THR* 3.9 24.5 - - + +
169A ILE* 4.6 0.6 - - - +
172A ALA* 3.9 27.6 - - + -
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ILE* 2.9 35.0 + - - +
127A PHE* 3.7 8.8 - - - +
129A LEU* 1.3 76.0 - - - +
131A LYS* 1.3 63.8 + - - +
133A GLY* 2.9 14.7 + - - -
134A ALA 3.4 15.3 + - - +
136A ILE* 3.5 32.2 + - + +
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Residues in contact with LYS 131 (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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127A PHE* 3.0 54.0 + - + +
128A GLY 3.1 7.8 + - - +
130A GLU* 1.3 76.6 - - + +
132A LEU* 1.3 58.2 + - - +
133A GLY 3.1 3.0 + - - -
152A LYS 4.3 1.2 - - - +
154A ALA* 3.3 22.7 - - + +
155A HIS 3.9 21.1 + - - -
156A ILE* 3.7 20.4 - - + +
157A VAL 5.7 0.2 - - - +
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Residues in contact with LEU 132 (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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128A GLY 3.1 17.6 + - - +
129A LEU* 3.1 15.4 + - + +
131A LYS* 1.3 76.2 - - - +
133A GLY* 1.3 57.2 + - - +
134A ALA 3.6 1.1 - - - -
151A LEU* 3.4 21.9 - - + +
152A LYS* 2.8 45.1 + - - +
153A GLY* 4.2 0.9 - - - -
154A ALA 4.1 3.6 - - - +
156A ILE* 3.9 16.2 - - + -
169A ILE* 4.0 19.5 - - + +
172A ALA* 4.0 27.6 - - + -
173A ALA* 4.1 8.5 - - + +
176A ALA* 4.9 2.2 - - + -
180A THR* 3.4 26.5 - - + +
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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