Contacts of the helix formed by residues 117 - 137 (chain B) in PDB entry 3SE4
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 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B PRO* 1.4 77.4 - - - +
120B LEU* 3.0 27.7 + - - +
121B THR* 2.5 44.9 + - - +
124B ARG* 5.7 2.0 + - - +
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Residues in contact with PRO 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B MET* 4.1 13.6 - - - +
54B HIS* 6.2 6.3 - - + -
117B SER* 1.4 98.2 - - - +
119B ALA* 1.3 60.5 + - + +
120B LEU* 5.5 0.2 - - + -
121B THR* 3.1 17.9 - - + +
122B LEU 4.0 1.0 + - - -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A THR* 4.9 12.3 - - - +
182A SER* 5.6 2.2 - - - -
57B SER* 5.7 4.5 - - - +
58B VAL* 6.3 0.4 - - - +
61B GLU* 3.2 46.6 - - + +
118B PRO* 1.3 80.9 - - + +
120B LEU* 1.3 60.2 + - - +
121B THR 3.6 0.2 - - - -
122B LEU* 3.5 7.4 - - - +
123B ARG* 3.4 21.7 + - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 4.4 26.3 - - + +
94A THR* 4.6 17.9 - - + +
96A PHE* 4.5 28.7 - - + -
97A ARG* 5.1 4.0 - - + +
117B SER* 3.0 29.4 + - - +
118B PRO* 5.5 0.4 - - + -
119B ALA* 1.3 77.6 - - - +
121B THR* 1.3 63.9 + - - +
122B LEU 3.3 0.2 - - - -
123B ARG* 3.2 9.6 + - - +
124B ARG* 3.2 45.9 + - - +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 3.4 18.0 - - + +
43B GLU* 4.6 5.2 + - - +
44B MET* 3.8 19.5 - - - -
117B SER* 2.5 40.8 + - - +
118B PRO* 3.1 12.8 - - + +
120B LEU* 1.3 71.3 - - - +
122B LEU* 1.3 76.0 + - - +
124B ARG* 3.4 21.7 + - - +
125B TYR* 3.1 22.7 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 4.4 20.4 - - + -
41B PRO* 4.4 3.6 - - + -
44B MET* 3.3 35.9 - - + -
58B VAL* 3.5 15.7 - - + +
61B GLU* 3.2 37.0 - - + -
62B MET* 4.3 24.9 - - + +
65B GLN* 6.0 0.7 - - + -
118B PRO 4.5 0.2 - - - +
119B ALA* 3.5 14.4 - - - +
121B THR* 1.3 83.1 - - - +
123B ARG* 1.3 57.5 + - + +
125B TYR* 3.0 24.0 - - + +
126B PHE* 3.1 24.1 + - + -
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 4.3 18.3 - - + -
96A PHE* 2.8 42.9 - - - -
131A LEU* 3.9 7.3 - - + +
132A ASP* 2.6 39.1 + - - -
135A SER* 5.3 0.4 - - - -
179A LEU* 5.1 0.8 - - - +
181A THR* 3.2 15.8 + - - -
182A SER* 2.7 23.0 + - - +
61B GLU* 2.6 30.4 + - - +
64B GLN* 3.3 8.7 - - - +
65B GLN* 4.6 14.4 + - + +
119B ALA* 3.4 11.5 + - - +
120B LEU* 3.2 10.1 + - - +
121B THR 3.2 0.8 - - - -
122B LEU* 1.3 74.0 - - + +
124B ARG* 1.3 65.5 + - - +
125B TYR 3.0 1.3 - - - -
126B PHE* 3.3 9.3 + - - +
127B GLN* 2.9 22.0 + - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 4.0 23.9 + - - +
70A TYR* 3.4 41.3 + - + +
71A GLU* 4.2 6.8 - - - +
117B SER* 5.7 2.2 + - - +
120B LEU* 3.2 31.9 + - - +
121B THR* 3.4 23.3 + - - +
123B ARG* 1.3 78.9 - - - +
125B TYR* 1.3 65.8 + - - +
127B GLN* 3.2 15.2 + - - +
128B GLY* 3.2 8.8 + - - -
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.5 25.8 - - + +
39B ARG 4.1 1.8 - - - +
40B PHE* 3.3 52.3 - + + -
41B PRO* 3.8 11.0 - - + -
121B THR 3.1 10.7 + - - +
122B LEU* 3.0 11.9 - - - +
124B ARG* 1.3 80.5 - - - +
126B PHE* 1.3 96.4 + + - +
128B GLY* 3.0 18.9 + - - -
129B ILE* 3.5 30.7 + - + +
149B GLU* 2.5 33.1 + - - +
150B ILE* 4.8 1.7 - - + +
153B SER* 2.7 15.2 + - - -
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 4.4 2.0 - - + -
40B PHE* 5.7 0.2 - + - -
62B MET* 3.9 30.5 - - + -
65B GLN* 3.6 56.3 - - + +
66B ILE* 4.0 15.9 - - + -
69B LEU* 4.6 13.2 - - + -
122B LEU* 3.1 30.8 + - + +
123B ARG 3.3 6.9 + - - +
125B TYR* 1.3 96.4 - + - +
127B GLN* 1.3 63.8 + - - +
129B ILE* 3.4 10.4 + - + +
130B ARG* 3.2 24.4 + - - +
150B ILE* 3.6 27.4 - - + -
153B SER* 6.3 1.1 - - - -
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.9 13.1 - - - +
68A ASN* 2.9 36.8 + - - +
70A TYR* 2.8 35.0 - - + -
131A LEU* 4.1 11.4 - - + +
123B ARG 2.9 12.8 + - - +
124B ARG* 3.2 10.0 + - - +
126B PHE* 1.3 74.1 - - - +
128B GLY* 1.3 67.6 + - - +
130B ARG* 2.8 10.0 + - + +
131B VAL* 2.7 41.8 + - + +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 5.1 0.2 + - - -
38B PHE* 4.8 5.6 - - - -
124B ARG 3.2 5.4 + - - -
125B TYR 3.0 9.7 + - - -
127B GLN* 1.3 77.7 - - - +
129B ILE* 1.3 53.3 + - - +
131B VAL* 3.0 6.4 + - - +
132B TYR* 2.6 41.0 + - - +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.8 25.1 - - + -
69B LEU* 4.0 11.7 - - + -
125B TYR* 3.6 49.4 - - + +
126B PHE* 3.4 11.6 + - + +
127B GLN 3.1 0.2 - - - -
128B GLY* 1.3 76.7 - - - +
130B ARG* 1.3 61.7 + - - +
132B TYR* 4.0 0.7 - - - +
133B LEU* 3.1 30.9 + - + +
146B VAL* 3.5 38.8 - - + -
149B GLU* 4.1 12.8 - - + -
150B ILE* 4.3 14.4 - - + -
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 3.8 25.0 - - + +
65B GLN* 3.7 18.6 - - - +
68B SER* 3.2 36.4 + - - -
69B LEU* 3.4 40.5 - - - +
72B THR* 4.8 7.9 - - - +
126B PHE* 3.2 15.2 + - - +
127B GLN* 2.8 16.9 + - + +
129B ILE* 1.3 76.4 - - - +
131B VAL* 1.3 61.9 + - + +
133B LEU* 3.8 7.5 - - - +
134B LYS* 3.5 16.6 + - - +
138B TYR* 4.5 8.9 + - - -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 5.6 0.2 - - - +
127B GLN* 2.7 41.5 + - + +
128B GLY* 3.4 7.0 - - - +
130B ARG* 1.3 71.4 - - + +
132B TYR* 1.3 58.3 + - - +
133B LEU 2.8 4.9 - - - -
134B LYS* 2.7 29.9 + - + -
135B GLU* 2.8 38.5 + - + +
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Residues in contact with TYR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASP* 2.5 34.5 + - - +
35B ARG 4.7 1.1 - - - -
36B ARG* 3.2 62.3 - - + +
38B PHE* 3.8 26.2 - + + -
128B GLY 2.6 22.1 + - - +
129B ILE 4.0 1.8 - - - +
131B VAL* 1.3 72.8 - - - +
133B LEU* 1.3 70.2 + - + +
135B GLU* 3.5 6.3 - - - +
136B LYS* 3.1 30.0 + - + +
142B ALA* 3.8 30.4 - - + +
145B VAL* 3.6 14.9 - - + +
146B VAL* 4.4 1.8 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.4 13.2 - - + -
129B ILE 3.1 18.5 + - - +
130B ARG* 3.8 6.5 - - - +
131B VAL 2.7 1.4 + - - -
132B TYR* 1.3 79.8 - - + +
134B LYS* 1.3 66.7 + - - +
135B GLU 2.9 1.7 + - - -
136B LYS* 3.0 3.1 + - - +
137B LYS 2.7 21.1 + - - -
138B TYR* 3.2 34.1 + - + +
142B ALA* 3.5 26.2 - - + +
143B TRP* 4.2 28.7 - - + +
146B VAL* 3.2 31.2 - - + -
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG 3.5 10.4 + - - +
131B VAL* 2.7 17.3 + - + +
133B LEU* 1.3 74.6 - - - +
135B GLU* 1.3 66.0 + - + +
137B LYS* 3.0 11.8 + - - +
138B TYR* 4.2 19.2 - - + +
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 2.9 39.0 + - - +
131B VAL* 2.8 36.8 + - + +
132B TYR* 3.5 5.6 - - - +
134B LYS* 1.3 73.9 - - + +
136B LYS* 1.3 56.5 + - - +
137B LYS* 2.5 20.8 + - - +
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASP* 5.4 6.5 - - + +
132B TYR* 3.1 25.2 + - + +
133B LEU 3.0 3.7 + - - +
135B GLU* 1.3 75.9 - - - +
137B LYS* 1.3 68.3 + - - +
138B TYR 3.6 0.4 - - - -
139B SER* 3.5 16.3 - - - +
142B ALA* 3.7 23.1 - - + -
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU 2.7 6.3 + - - -
134B LYS* 3.3 12.1 - - - +
135B GLU 2.5 14.2 + - - +
136B LYS* 1.3 74.5 - - - +
138B TYR* 1.3 72.1 + - + +
139B SER* 2.8 5.0 + - - -
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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