Contacts of the helix formed by residues 122 - 135 (chain L) in PDB entry 1R4N
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 122 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120L THR 3.3 6.3 + - - +
121L ASP* 1.3 75.3 - - - +
123L VAL* 1.3 68.0 + - - +
124L GLU* 3.0 22.5 + - + +
125L ARG* 2.9 27.8 + - + +
126L ILE* 3.3 6.6 + - - +
152L ASP 4.7 2.5 - - - +
153L GLU* 3.0 39.9 + - - +
154L LYS 2.9 15.3 - - - +
155L THR* 4.0 2.0 - - - +
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Residues in contact with VAL 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L ASP 3.5 1.0 + - - -
122L LYS* 1.3 70.6 - - - +
124L GLU* 1.3 55.5 + - - +
126L ILE* 2.6 42.9 + - + +
127L LYS* 3.2 8.3 + - - +
143L LEU* 4.3 12.3 - - + -
150L MET* 3.3 32.8 - - + +
151L ASN 3.0 27.4 - - - +
152L ASP* 3.7 9.2 - - + +
154L LYS 2.6 19.8 + - - +
155L THR 4.2 5.4 - - - +
156L ALA* 5.2 0.2 - - - -
159L TYR* 3.6 26.0 - - + -
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Residues in contact with GLU 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L LYS* 4.3 15.4 + - + +
123L VAL* 1.3 79.1 - - - +
125L ARG* 1.3 58.9 + - - +
127L LYS* 3.5 9.6 + - - +
128L GLU* 3.4 27.5 + - + +
138L PRO* 5.5 1.2 - - - +
152L ASP* 2.8 43.5 + - + +
153L GLU* 4.9 9.0 - - - +
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Residues in contact with ARG 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237G TYR* 4.5 12.5 + - - -
120L THR* 4.3 7.5 + - - +
121L ASP* 3.5 44.0 + - + +
122L LYS* 2.9 24.8 + - + +
124L GLU* 1.3 75.7 - - - +
126L ILE* 1.3 68.1 + - - +
127L LYS 3.0 1.8 - - - -
128L GLU* 2.9 32.5 + - + +
129L ARG* 3.0 48.7 + - - +
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Residues in contact with ILE 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L VAL* 5.8 0.4 - - + -
115L ILE* 4.0 6.5 - - + +
117L ILE* 3.2 36.3 - - + -
121L ASP* 4.3 3.1 - - + +
122L LYS 3.5 8.3 - - - +
123L VAL* 2.6 39.0 + - + +
125L ARG* 1.3 72.5 - - - +
127L LYS* 1.3 57.8 + - - +
129L ARG* 3.3 17.1 - - - +
130L VAL* 3.4 12.5 + - + +
143L LEU* 4.1 11.0 - - + -
150L MET* 5.2 0.9 - - + -
156L ALA* 4.0 29.4 - - + -
161L ILE* 4.2 12.8 - - + -
167L LEU* 4.1 21.1 - - + -
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Residues in contact with LYS 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L VAL* 3.2 10.5 + - - +
124L GLU* 3.5 8.7 - - - +
125L ARG 3.0 0.4 - - - -
126L ILE* 1.3 74.4 - - - +
128L GLU* 1.3 65.9 + - - +
129L ARG 3.0 2.0 - - - -
130L VAL* 2.8 16.4 + - - +
131L GLU 2.9 10.6 + - - -
138L PRO* 4.1 25.4 + - + +
141L GLN* 3.3 52.6 + - + +
142L ARG* 4.7 8.3 - - - +
143L LEU* 3.9 28.7 - - + +
150L MET 4.8 6.5 + - - -
152L ASP* 3.5 42.2 + - + +
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Residues in contact with GLU 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G ARG* 4.4 14.6 + - - -
270G LYS* 5.1 4.5 - - - +
273G ASN* 3.0 35.7 + - - +
124L GLU* 3.4 20.3 + - + +
125L ARG* 2.9 26.9 + - + +
127L LYS* 1.3 75.7 - - - +
129L ARG* 1.3 60.4 + - + +
131L GLU* 3.3 6.4 + - - +
132L GLU* 2.8 25.8 + - - +
138L PRO* 4.5 13.9 - - + +
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Residues in contact with ARG 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236G THR* 5.1 7.7 - - - +
237G TYR* 3.7 38.8 + - - +
273G ASN* 5.0 7.8 + - - -
115L ILE* 3.3 36.1 - - + +
116L ASP 4.7 8.2 + - - -
117L ILE* 4.6 5.4 - - + -
121L ASP* 4.6 3.4 + - - +
125L ARG* 3.0 52.8 + - - +
126L ILE* 3.3 12.3 - - - +
128L GLU* 1.3 81.6 - - - +
130L VAL* 1.3 61.4 + - - +
132L GLU* 3.4 27.9 + - - +
133L LYS* 3.3 23.0 + - - +
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Residues in contact with VAL 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L VAL* 3.3 36.3 - - + -
113L ILE* 3.6 19.7 - - + -
115L ILE* 3.6 2.5 - - + -
126L ILE* 3.5 16.6 - - + +
127L LYS* 2.8 8.8 + - - +
129L ARG* 1.3 75.7 - - - +
131L GLU* 1.3 54.9 + - - +
133L LYS* 3.0 4.2 + - - +
134L GLU* 2.7 33.3 + - + +
136L ILE* 4.2 21.1 - - + -
141L GLN* 3.3 22.9 - - - +
143L LEU* 5.3 3.1 - - + -
169L LEU* 4.2 8.7 - - + -
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Residues in contact with GLU 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G LEU* 3.6 3.8 - - - +
270G LYS 4.9 4.3 - - - +
273G ASN* 3.6 18.7 + - - +
274G THR* 3.7 18.7 + - - +
127L LYS 2.9 11.3 + - - +
128L GLU* 3.6 6.1 - - - +
130L VAL* 1.3 76.0 - - - +
132L GLU* 1.3 60.1 + - - +
135L GLY* 2.8 29.8 + - - +
136L ILE 3.4 28.0 - - - +
137L PRO* 3.8 8.1 - - - +
138L PRO* 3.2 33.5 - - + +
141L GLN* 4.2 0.2 - - - +
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Residues in contact with GLU 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G LEU* 3.6 16.6 - - - +
236G THR* 4.0 11.5 - - - +
240G LYS* 3.0 29.2 + - - +
273G ASN* 3.6 33.0 - - - +
274G THR* 4.9 4.4 - - - +
277G ASN 5.8 0.2 - - - +
128L GLU 2.8 16.1 + - - +
129L ARG* 3.5 27.4 + - - +
130L VAL 3.1 0.2 - - - -
131L GLU* 1.3 80.6 - - - +
133L LYS* 1.3 64.2 + - + +
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Residues in contact with LYS 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G LEU* 3.8 11.8 - - - +
111L LYS* 5.5 0.2 + - - -
113L ILE* 4.5 22.9 - - + -
114L GLU* 3.3 34.6 + - - +
115L ILE* 5.6 2.2 - - + -
129L ARG 3.3 9.6 + - - +
130L VAL 3.0 6.2 + - - +
132L GLU* 1.3 87.6 - - + +
134L GLU* 1.3 67.6 + - + +
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Residues in contact with GLU 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178G ASN 3.4 25.3 - - - +
179G ALA* 3.6 7.6 - - - -
180G LEU* 3.9 5.3 + - - -
107L THR* 5.5 5.4 - - - -
111L LYS* 2.7 47.5 + - - +
113L ILE* 3.3 32.8 - - + +
130L VAL* 2.7 17.5 + - + +
133L LYS* 1.3 82.0 - - - +
135L GLY* 1.3 60.2 + - - +
136L ILE* 3.7 25.2 - - + +
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Residues in contact with GLY 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178G ASN* 3.9 7.6 - - - +
179G ALA 3.7 14.9 + - - +
180G LEU* 3.1 24.2 - - - +
274G THR* 5.7 0.4 - - - -
131L GLU* 2.8 24.0 + - - -
134L GLU* 1.3 74.2 - - - +
136L ILE* 1.3 60.0 - - - +
137L PRO* 3.2 12.8 - - - +
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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