Contacts of the helix formed by residues 115 - 135 (chain L) in PDB entry 1N13
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 SER 115 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88L THR* 4.5 4.5 - - - -
90L SER* 3.1 8.5 + - - -
114L CYS* 1.3 73.8 - - - +
116L LYS* 1.3 64.6 + - - +
117L LYS* 3.7 7.4 + - - +
118L GLU* 3.3 27.3 + - - +
119L ALA* 3.0 20.6 + - - +
147L GLU* 3.6 12.1 - - - -
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Residues in contact with LYS 116 (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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90L SER* 3.2 11.5 + - - -
115L SER* 1.3 71.2 - - - +
117L LYS* 1.3 70.0 + - + +
119L ALA* 3.4 3.3 + - - +
120L GLU* 3.0 37.7 + - - +
145L ALA* 3.5 39.8 - - + +
146L VAL* 3.7 8.5 - - - +
147L GLU* 2.9 33.7 + - + +
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Residues in contact with LYS 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115L SER* 3.3 7.4 + - - +
116L LYS* 1.3 92.6 - - - +
118L GLU* 1.3 63.2 + - - +
120L GLU* 3.4 7.1 + - - +
121L LYS* 2.9 28.9 + - - +
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Residues in contact with GLU 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L CYS* 4.4 14.8 - - + -
115L SER* 3.3 21.9 + - - +
117L LYS* 1.3 80.8 - - + +
119L ALA* 1.3 60.6 + - - +
121L LYS* 3.5 29.7 - - - +
122L THR* 2.9 36.6 + - - +
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Residues in contact with ALA 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L SER* 3.8 20.4 - - - -
91L ALA 4.6 4.3 - - - +
92L ALA* 3.7 13.7 - - + +
110L TYR* 3.8 27.0 - - + -
114L CYS* 4.0 4.2 - - - -
115L SER 3.0 18.1 + - - +
116L LYS* 3.6 4.9 - - - +
117L LYS 3.3 0.2 - - - -
118L GLU* 1.3 78.4 - - - +
120L GLU* 1.3 56.7 + - - +
122L THR* 3.4 1.9 + - - -
123L VAL* 2.9 31.0 + - - +
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Residues in contact with GLU 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L ALA* 4.0 3.1 - - - +
116L LYS* 3.0 25.5 + - - +
117L LYS* 3.8 6.7 - - - +
119L ALA* 1.3 74.2 - - - +
121L LYS* 1.3 65.9 + - - +
123L VAL* 3.4 7.2 - - + +
124L ARG* 3.0 38.0 + - - +
143L SER* 2.7 46.9 + - - +
144L ILE* 3.7 2.7 + - - +
145L ALA* 3.8 19.0 + - + +
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Residues in contact with LYS 121 (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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117L LYS 2.9 18.7 + - - +
118L GLU* 3.5 32.3 - - - +
119L ALA 3.3 0.2 - - - -
120L GLU* 1.3 76.3 - - - +
122L THR* 1.3 68.2 + - - +
124L ARG* 3.5 7.8 + - - +
125L GLU* 3.1 24.7 + - + +
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Residues in contact with THR 122 (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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29I THR* 5.7 4.5 - - + -
110L TYR* 3.8 39.5 + - + +
118L GLU* 2.9 19.2 + - - +
119L ALA 3.7 3.4 - - - -
121L LYS* 1.3 83.8 + - - +
123L VAL* 1.3 57.6 + - - +
125L GLU* 3.2 8.8 + - + +
126L MET* 3.0 34.9 + - + +
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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
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92L ALA* 3.6 25.6 - - + +
93L ILE 4.0 6.5 - - - +
94L SER* 2.8 31.7 + - - +
108L MET* 3.3 36.6 - - + +
109L GLU 3.7 16.6 - - - -
110L TYR* 3.9 7.0 - - + -
119L ALA 2.9 11.2 + - - +
120L GLU* 3.4 11.9 - - - +
122L THR* 1.3 74.5 - - - +
124L ARG* 1.3 70.8 + - + +
126L MET* 3.4 9.5 + - - +
127L ALA 3.3 11.6 + - - -
143L SER* 4.5 1.3 - - - -
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Residues in contact with ARG 124 (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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94L SER* 4.2 5.4 - - - -
120L GLU* 3.0 34.3 + - - +
121L LYS* 3.8 6.3 - - - +
123L VAL* 1.3 75.4 - - - +
125L GLU* 1.3 63.9 + - - +
127L ALA* 3.2 1.9 + - - +
128L LYS* 3.1 18.6 + - - +
141L ILE* 2.9 65.7 + - + +
143L SER* 2.8 46.8 + - - +
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Residues in contact with GLU 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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28I GLU* 4.8 4.3 - - - +
121L LYS* 3.1 16.0 + - + +
122L THR* 3.4 12.1 - - + +
124L ARG* 1.3 77.4 - - - +
126L MET* 1.3 56.5 + - + +
128L LYS* 3.0 44.3 + - - +
129L ILE* 2.9 57.4 + - + +
132L GLU* 5.0 0.5 - - - +
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Residues in contact with MET 126 (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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29I THR* 3.8 21.5 - - + +
30I PRO* 6.2 0.2 - - + -
31I LEU* 3.6 35.2 - - + +
32I ASN* 3.0 38.3 - - - +
108L MET* 3.7 15.3 - - + +
109L GLU 3.6 19.5 - - - +
110L TYR* 4.1 13.5 - - + -
122L THR* 3.0 34.8 + - + +
123L VAL* 3.6 15.3 - - - +
124L ARG 3.2 0.2 - - - -
125L GLU* 1.3 77.2 - - + +
127L ALA* 1.3 56.2 + - - +
129L ILE* 3.4 1.5 + - + -
130L GLY* 3.0 15.2 + - - -
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Residues in contact with ALA 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L SER* 3.5 23.8 - - - +
96L ALA* 3.8 36.4 - - + +
106L LEU* 4.0 6.5 - - - +
108L MET* 3.7 12.2 - - + +
123L VAL 3.3 2.4 + - - -
124L ARG 3.2 8.5 + - - +
126L MET* 1.3 74.3 - - - +
128L LYS* 1.3 67.0 + - - +
130L GLY* 3.1 11.0 + - - +
131L PHE* 3.1 9.5 + - - +
141L ILE* 4.2 7.2 - - + -
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Residues in contact with LYS 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124L ARG 3.1 13.1 + - - +
125L GLU* 3.0 42.4 + - - +
127L ALA* 1.3 77.6 - - - +
129L ILE* 1.3 60.3 + - - +
131L PHE* 3.2 5.3 + - - +
132L GLU* 3.0 50.7 + - + +
138L LEU* 4.4 18.8 - - + -
141L ILE* 4.0 10.9 - - + +
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Residues in contact with ILE 129 (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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28I GLU* 3.4 45.5 - - + +
29I THR* 5.0 3.8 - - + -
32I ASN* 3.6 33.7 - - + +
125L GLU* 2.9 46.1 + - + +
126L MET* 3.6 4.7 - - - +
128L LYS* 1.3 74.3 - - - +
130L GLY* 1.3 57.9 + - - +
132L GLU* 3.1 17.2 + - + +
133L MET* 2.8 43.5 + - + +
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Residues in contact with GLY 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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32I ASN* 4.3 4.5 - - - -
35I ASP* 4.2 5.6 - - - -
106L LEU* 3.4 28.3 - - - -
126L MET 3.0 12.3 + - - -
127L ALA 3.1 0.6 + - - -
129L ILE* 1.3 77.7 - - - +
131L PHE* 1.3 59.4 + - - +
133L MET* 3.4 7.1 + - - +
134L ARG* 3.2 33.7 + - - +
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Residues in contact with PHE 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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96L ALA* 3.6 38.4 - - + -
97L ILE 4.1 2.9 - - - -
98L PRO* 3.6 32.3 - - + -
104L CYS 3.7 16.2 - - - -
106L LEU* 3.8 21.1 - - + -
127L ALA 3.1 7.8 + - - +
128L LYS* 3.2 7.8 + - - +
130L GLY* 1.3 74.4 - - - +
132L GLU* 1.3 57.3 + - + +
134L ARG* 3.2 5.6 + - - +
135L GLY* 2.7 30.0 + - - -
136L TRP* 3.1 54.4 + + + +
137L GLU 3.7 4.7 - - - -
138L LEU* 3.8 26.0 - - + -
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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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28I GLU* 4.6 5.2 - - - +
125L GLU* 5.0 0.3 - - - +
128L LYS* 3.0 45.9 + - + +
129L ILE* 3.1 26.5 + - + +
131L PHE* 1.3 78.3 - - + +
133L MET* 1.3 62.1 + - + +
135L GLY* 3.3 12.5 + - - +
136L TRP 5.6 0.2 - - - -
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Residues in contact with MET 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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25I SER* 4.1 3.1 - - - +
26I GLU 3.9 17.0 - - - +
27I GLY* 5.0 2.9 - - - -
32I ASN* 3.6 30.7 - - - +
35I ASP* 5.1 3.4 - - - +
36I GLY* 3.8 20.6 - - - -
39I LEU* 4.9 12.7 - - + +
129L ILE* 2.8 39.4 + - + +
130L GLY* 3.7 9.6 - - - +
131L PHE 3.2 0.2 - - - -
132L GLU* 1.3 79.6 - - + +
134L ARG* 1.3 59.7 + - - +
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Residues in contact with ARG 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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35I ASP* 2.8 42.6 + - - -
39I LEU* 3.8 24.2 - - + +
44I GLY 3.0 24.0 + - - -
45I ASN* 2.8 18.6 + - - -
54L ILE* 4.2 2.3 - - - +
104L CYS* 5.3 0.2 - - - -
106L LEU* 3.6 22.3 - - - +
130L GLY 3.2 20.9 + - - +
131L PHE* 3.2 11.9 + - - +
132L GLU 3.2 0.2 - - - -
133L MET* 1.3 76.6 - - - +
135L GLY* 1.3 62.2 + - - +
136L TRP* 3.4 54.2 + - + +
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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
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131L PHE 2.7 7.4 + - - -
132L GLU* 3.3 11.9 + - - -
134L ARG* 1.3 80.4 - - - +
136L TRP* 1.3 64.4 + - - +
137L GLU 4.2 0.5 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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