Contacts of the helix formed by residues 119 - 131 (chain A) in PDB entry 1REC
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 LYS 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A SER* 1.3 74.5 - - - +
120A ASN* 1.3 66.0 + - - +
122A VAL* 3.3 5.1 + - + +
123A LEU* 3.2 21.8 + - + +
152A ALA* 5.3 6.5 - - + +
153A GLU* 2.8 40.7 + - - +
156A TRP* 3.5 47.2 - - + +
163A ASP* 2.7 58.1 + - + +
165A ASP 4.5 1.0 + - - -
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Residues in contact with ASN 120 (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 SER* 2.5 29.2 + - - -
119A LYS* 1.3 77.1 - - - +
121A GLU* 1.3 65.5 + - - +
123A LEU* 3.4 11.6 + - + +
124A GLU* 3.0 30.3 + - - +
163A ASP 5.8 0.6 + - - -
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Residues in contact with GLU 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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109A TYR 3.2 17.3 - - - +
110A ASP* 3.9 0.5 - - - +
111A VAL* 3.3 22.5 + - + +
112A ASP* 3.1 29.9 + - - +
116A THR 3.1 3.3 - - - +
117A ILE* 3.1 5.0 - - + -
118A SER* 2.9 39.9 + - - +
120A ASN* 1.3 80.2 - - - +
122A VAL* 1.3 65.1 + - - +
124A GLU* 3.1 6.5 + - - +
125A ILE* 3.0 26.7 + - - +
501A CA 2.3 31.0 - - - -
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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
----------------------------------------------------------
109A TYR* 4.1 18.8 - - + -
117A ILE* 3.5 18.6 - - + -
118A SER 3.3 14.6 + - - +
119A LYS* 3.6 7.0 - - + +
121A GLU* 1.3 75.8 - - - +
123A LEU* 1.3 57.9 + - - +
125A ILE* 3.4 1.0 + - - +
126A VAL* 2.9 39.1 + - + +
152A ALA* 4.2 13.7 - - + +
155A ILE* 4.0 38.4 - - + -
156A TRP* 4.0 19.5 - - + -
167A LEU* 5.5 2.2 - - + -
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Residues in contact with LEU 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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119A LYS* 3.2 12.6 + - + +
120A ASN* 3.6 13.0 - - + +
122A VAL* 1.3 80.3 - - - +
124A GLU* 1.3 53.2 + - - +
126A VAL 3.9 0.2 - - - -
127A THR* 2.7 47.1 + - - +
148A PRO* 3.8 32.1 - - + +
149A GLU* 3.8 19.7 - - + +
152A ALA* 3.9 12.3 - - + +
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Residues in contact with GLU 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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64A ALA* 5.8 2.3 - - - +
68A HIS* 3.3 33.3 + - - +
111A VAL* 4.0 17.6 - - + +
120A ASN 3.0 15.0 + - - +
121A GLU* 3.1 12.5 + - - +
123A LEU* 1.3 77.7 - - - +
125A ILE* 1.3 63.4 + - - +
127A THR* 3.6 6.2 - - - -
128A ALA* 3.2 21.8 + - - +
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Residues in contact with ILE 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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65A TYR* 6.4 0.4 - - + -
68A HIS* 3.6 32.8 - - + +
71A ARG* 3.7 0.2 - - - +
108A LEU* 3.4 40.6 - - + +
109A TYR* 3.6 46.0 - - + -
111A VAL* 3.7 12.3 - - + -
121A GLU 3.0 14.8 + - - +
124A GLU* 1.3 72.2 - - - +
126A VAL* 1.3 60.4 + - - +
128A ALA* 3.3 6.2 + - + +
129A ILE* 2.9 45.4 + - + +
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Residues in contact with VAL 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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109A TYR* 4.7 9.2 - - + +
122A VAL* 2.9 27.4 + - + +
123A LEU* 3.9 4.0 - - - +
125A ILE* 1.3 75.4 - - - +
127A THR* 1.3 58.5 + - - +
129A ILE* 3.4 9.8 + - + +
130A PHE* 2.9 33.6 + - + +
148A PRO* 3.6 25.6 - - + +
151A ARG* 3.3 28.7 - - + -
152A ALA* 4.4 2.9 - - + -
155A ILE* 3.8 28.9 - - + -
185A LEU 5.0 1.6 - - - +
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Residues in contact with THR 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 LEU* 2.7 29.0 + - - +
124A GLU* 3.6 8.0 - - - -
126A VAL* 1.3 78.7 - - - +
128A ALA* 1.3 58.8 + - - +
130A PHE* 3.4 3.6 + - - +
131A LYS* 3.0 42.0 + - + +
148A PRO* 3.4 29.3 - - + +
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Residues in contact with ALA 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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61A ASP 4.8 0.2 - - - +
64A ALA* 3.8 15.5 - - + -
65A TYR* 3.8 32.9 + - + +
68A HIS* 3.9 13.7 - - + +
124A GLU 3.2 11.7 + - - +
125A ILE* 3.3 8.7 + - + +
127A THR* 1.3 76.3 - - - +
129A ILE* 1.3 64.4 + - - +
131A LYS* 3.3 20.8 + - - +
132A MET* 3.6 10.9 + - - +
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Residues in contact with ILE 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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65A TYR* 4.2 19.3 - - + -
109A TYR* 3.8 12.1 - - - +
125A ILE* 2.9 41.4 + - + +
126A VAL* 3.6 9.4 - - + +
128A ALA* 1.3 75.9 - - + +
130A PHE* 1.3 61.0 + - + +
132A MET* 3.0 31.9 + - + +
133A ILE* 3.7 6.9 + - + +
185A LEU 5.9 0.9 - - - +
186A ILE 5.1 0.2 - - - -
187A GLN 3.8 18.2 - - - +
188A PHE* 3.8 15.7 - - + +
190A PRO* 6.1 0.7 - - + -
193A VAL* 4.1 31.6 - - + -
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Residues in contact with PHE 130 (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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126A VAL* 2.9 29.6 + - + +
127A THR 3.4 7.6 - - - +
129A ILE* 1.3 79.4 - - + +
131A LYS* 1.3 56.1 + - + +
132A MET 3.1 0.4 - - - -
133A ILE* 3.2 41.2 + - + +
138A THR* 5.1 8.0 + - + -
141A LEU* 3.5 26.5 - - + -
145A GLU 3.3 26.0 - - - -
146A ASN 3.6 17.3 - - - -
147A THR* 3.9 7.0 - - - -
148A PRO* 4.0 20.2 - - + -
151A ARG* 4.1 28.0 - - + -
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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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60A ALA* 3.2 4.9 - - - +
61A ASP* 2.9 72.2 + - + +
64A ALA* 4.4 18.9 - - + +
127A THR* 3.0 32.9 - - + +
128A ALA* 3.4 11.0 - - - +
129A ILE 3.1 0.4 - - - -
130A PHE* 1.3 76.1 - - + +
132A MET* 1.3 57.1 + - - +
133A ILE 3.3 3.6 + - - +
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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