Contacts of the helix formed by residues 117 - 130 (chain B) in PDB entry 4L1O
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 PHE 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B LEU* 4.4 10.3 - - + -
36B ILE* 3.7 29.4 - - + -
43B LEU* 3.7 29.2 - - + -
47B LEU* 5.2 0.7 - - + -
62B GLU* 2.8 13.2 + - + +
63B VAL* 3.9 27.1 - - + -
66B VAL* 3.6 33.4 - - + -
116B PRO* 1.3 79.4 - - - +
118B ASN* 1.3 59.7 + - - +
120B THR* 2.9 2.3 + - - -
121B ILE* 2.8 60.3 + - + +
145B MET* 4.0 16.1 - - + +
149B LEU* 4.1 14.8 - - + -
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Residues in contact with ASN 118 (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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62B GLU* 3.1 33.6 + - + +
65B TYR* 3.9 9.0 - - - +
66B VAL* 3.8 11.3 - - + +
115B TYR* 3.9 11.4 - - + +
117B PHE* 1.3 80.3 - - - +
119B LEU* 1.3 63.9 + - - +
120B THR 3.1 1.0 + - - -
122B GLN* 2.8 58.2 + - - +
123B PRO* 3.2 3.6 - - - +
412B TYR* 5.0 1.6 + - - -
601B 1VL 3.5 34.2 - - - -
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Residues in contact with LEU 119 (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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109B VAL* 4.2 3.1 - - - +
110B ILE 4.6 0.7 - - - +
111B GLY* 3.4 15.8 - - - -
112B THR* 3.3 24.5 - - + +
114B ASN* 3.3 26.7 - - - +
115B TYR* 2.9 31.1 + - + +
118B ASN* 1.3 83.7 - - - +
120B THR* 1.3 59.6 + - - +
123B PRO* 3.9 13.5 - - - +
184B LEU* 5.4 0.5 - - - +
186B THR* 4.4 14.3 + - + +
209B GLU* 4.5 0.2 - - - +
412B TYR* 3.9 9.0 - - - +
601B 1VL 3.3 51.1 - - + +
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Residues in contact with THR 120 (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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109B VAL* 3.8 9.0 - - - +
111B GLY* 3.8 19.7 - - - -
112B THR 5.0 0.7 - - - +
116B PRO* 2.6 30.5 + - + +
117B PHE* 2.9 6.8 + - - -
119B LEU* 1.3 82.1 - - - +
121B ILE* 1.3 74.8 + - - +
122B GLN 3.6 0.7 - - - -
123B PRO* 3.6 3.0 - - - +
124B MET* 3.4 20.3 + - - +
136B LEU* 3.7 31.5 - - + +
138B PRO* 4.4 15.5 - - + -
139B SER 5.3 0.7 - - - +
149B LEU* 3.7 8.1 - - + +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.2 20.6 - - + -
36B ILE* 5.8 0.4 - - + -
66B VAL* 3.7 24.5 - - + -
117B PHE* 2.8 50.2 + - + +
120B THR* 1.3 85.1 - - - +
122B GLN* 1.3 58.3 + - - +
123B PRO 3.4 0.2 - - - -
124B MET* 3.2 9.3 + - + +
125B VAL* 2.8 33.8 + - + +
136B LEU* 4.2 11.7 - - + -
149B LEU* 4.1 8.1 - - + -
153B ILE* 3.8 28.0 - - + -
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Residues in contact with GLN 122 (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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65B TYR* 3.9 26.5 + - - +
66B VAL* 4.2 8.8 - - + +
69B GLU* 3.6 33.1 - - + +
117B PHE 4.2 0.2 + - - -
118B ASN* 2.8 51.4 + - - +
121B ILE* 1.3 74.6 - - - +
123B PRO* 1.3 66.1 - - + +
125B VAL* 3.4 15.0 + - - +
126B GLY* 3.4 9.0 + - - -
412B TYR* 4.7 2.1 - - + -
413B HIS* 3.3 38.7 + - + -
417B SER* 5.0 2.3 + - - -
601B 1VL 5.0 0.6 - - - -
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Residues in contact with PRO 123 (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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109B VAL* 3.9 19.7 - - + -
118B ASN 3.2 13.7 - - - +
119B LEU* 3.9 15.9 - - - +
120B THR 3.6 7.9 - - - +
122B GLN* 1.3 92.7 - - + +
124B MET* 1.3 61.3 + - - +
126B GLY* 3.2 3.3 + - - -
127B ALA* 3.1 17.8 + - - +
184B LEU* 4.0 24.0 - - + -
186B THR* 5.7 0.2 - - - +
412B TYR* 3.8 34.7 - - + +
421B PHE* 3.4 12.8 - - + -
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Residues in contact with MET 124 (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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32B LEU* 5.3 3.4 - - + -
109B VAL* 4.3 8.9 - - + +
120B THR 3.4 16.4 + - - +
121B ILE* 3.2 25.7 + - + +
123B PRO* 1.3 75.7 - - - +
125B VAL* 1.3 61.3 - - - +
127B ALA* 3.4 2.2 + - - +
128B ILE* 3.0 41.2 + - + +
134B VAL* 3.8 27.6 - - + +
136B LEU* 4.6 15.9 - - + -
153B ILE* 4.5 8.5 - - + -
157B LEU* 3.7 20.2 - - + -
162B TYR* 3.4 43.3 - - + +
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Residues in contact with VAL 125 (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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29B LEU* 3.7 21.0 - - + +
32B LEU* 3.8 16.6 - - + -
66B VAL* 4.5 4.0 - - + +
69B GLU* 4.1 12.6 - - + -
70B ILE* 3.6 35.7 - - + -
73B MET* 4.0 16.6 - - + -
121B ILE* 2.8 24.8 + - + +
122B GLN* 3.5 11.7 - - - +
124B MET* 1.3 73.0 - - - +
126B GLY* 1.3 59.4 + - - +
128B ILE* 3.3 4.8 + - - +
129B ALA* 2.9 28.4 + - - +
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Residues in contact with GLY 126 (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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73B MET* 3.8 23.9 - - - +
122B GLN 3.4 4.6 + - - -
123B PRO 3.2 7.6 + - - -
125B VAL* 1.3 78.8 - - - +
127B ALA* 1.3 60.5 + - - +
129B ALA* 3.2 4.7 + - - +
130B ALA* 3.1 22.7 + - - +
417B SER* 3.9 15.8 - - - +
418B PHE* 4.7 1.7 - - - -
421B PHE* 3.5 7.1 - - - -
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Residues in contact with ALA 127 (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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107B VAL* 4.1 19.7 - - + -
109B VAL* 5.2 0.2 - - + -
123B PRO 3.1 13.0 + - - +
124B MET 3.8 3.6 - - - +
125B VAL 3.3 0.2 - - - -
126B GLY* 1.3 72.3 - - - +
128B ILE* 1.3 64.4 + - - +
130B ALA 3.5 2.1 + - - -
132B ASN* 3.1 30.0 + - - +
134B VAL* 3.5 26.2 - - + -
421B PHE* 3.3 25.4 - - + -
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Residues in contact with ILE 128 (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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25B ARG* 3.6 18.0 - - + +
28B GLN* 4.0 17.9 - - + -
29B LEU* 4.0 14.8 - - + -
32B LEU* 3.9 24.9 - - + -
124B MET* 3.0 36.3 + - + +
125B VAL* 3.7 4.5 - - - +
127B ALA* 1.3 72.3 - - - +
129B ALA* 1.3 66.8 + - - +
131B GLY* 3.0 14.9 + - - -
132B ASN 4.3 6.9 - - - +
134B VAL* 4.2 3.6 - - + -
157B LEU* 4.3 17.0 - - + -
162B TYR* 3.6 35.1 + - + +
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Residues in contact with ALA 129 (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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25B ARG* 2.9 26.5 + - - +
29B LEU* 4.3 18.6 - - + +
73B MET* 3.8 22.9 - - + -
77B LEU* 3.2 23.2 - - + +
80B TRP* 5.8 0.9 - - + -
125B VAL 2.9 14.1 + - - +
126B GLY 3.4 9.2 - - - +
128B ILE* 1.3 77.1 - - - +
130B ALA* 1.3 55.5 + - - +
131B GLY 3.2 0.2 - - - -
418B PHE* 3.6 8.2 - - + -
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Residues in contact with ALA 130 (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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25B ARG* 3.3 10.7 + - - +
102B GLU 4.6 0.2 - - - -
103B PRO* 3.3 26.3 - - - +
126B GLY 3.1 9.4 + - - +
128B ILE 3.2 0.4 - - - -
129B ALA* 1.3 74.0 - - - +
131B GLY* 1.3 58.5 + - - +
132B ASN* 3.4 7.9 - - - +
418B PHE* 3.9 15.0 - - + +
421B PHE* 3.4 35.0 - - + +
422B SER* 3.4 16.4 + - - +
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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